rs145176864

Positions:

chr22-23573444-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_020070.4(IGLL1):c.464C>T(p.Pro155Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 1,613,066 control chromosomes in the GnomAD database, including 228 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 62 hom., cov: 32)

Exomes 𝑓: 0.012 ( 166 hom. )

Consequence

IGLL1
NM_020070.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.940

Variant links:

Genes affected

IGLL1 (HGNC:5870): (immunoglobulin lambda like polypeptide 1) The preB cell receptor is found on the surface of proB and preB cells, where it is involved in transduction of signals for cellular proliferation, differentiation from the proB cell to the preB cell stage, allelic exclusion at the Ig heavy chain gene locus, and promotion of Ig light chain gene rearrangements. The preB cell receptor is composed of a membrane-bound Ig mu heavy chain in association with a heterodimeric surrogate light chain. This gene encodes one of the surrogate light chain subunits and is a member of the immunoglobulin gene superfamily. This gene does not undergo rearrangement. Mutations in this gene can result in B cell deficiency and agammaglobulinemia, an autosomal recessive disease in which few or no gamma globulins or antibodies are made. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

IGLL1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038833618).

BP6

Variant 22-23573444-G-A is Benign according to our data. Variant chr22-23573444-G-A is described in ClinVar as [Benign]. Clinvar id is 439823.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0223 (3393/151964) while in subpopulation AFR AF= 0.0498 (2068/41488). AF 95% confidence interval is 0.0481. There are 62 homozygotes in gnomad4. There are 1669 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 62 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
IGLL1	NM_020070.4 linkuse as main transcript	c.464C>T	p.Pro155Leu	missense_variant	3/3	ENST00000330377.3	NP_064455.1
IGLL1	NM_001369906.1 linkuse as main transcript	c.467C>T	p.Pro156Leu	missense_variant	3/3		NP_001356835.1
IGLL1	NM_152855.3 linkuse as main transcript	c.*93C>T		3_prime_UTR_variant	2/2		NP_690594.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGLL1	ENST00000330377.3 linkuse as main transcript	c.464C>T	p.Pro155Leu	missense_variant	3/3	1	NM_020070.4	ENSP00000329312	P1	P15814-1
IGLL1	ENST00000249053.3 linkuse as main transcript	c.*93C>T		3_prime_UTR_variant	2/2	1		ENSP00000249053		P15814-2
	ENST00000458318.2 linkuse as main transcript	n.391-21G>A		intron_variant, non_coding_transcript_variant		3
IGLL1	ENST00000438703.1 linkuse as main transcript	c.467C>T	p.Pro156Leu	missense_variant	3/3	2		ENSP00000403391

Frequencies

GnomAD3 genomes

AF:

0.0223

AC:

3383

AN:

151846

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0498

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0214

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.00348

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.00481

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0108

Gnomad OTH

AF:

0.0229

GnomAD3 exomes

AF:

0.0143

AC:

3590

AN:

251226

Hom.:

AF XY:

0.0143

AC XY:

1943

AN XY:

135758

show subpopulations

Gnomad AFR exome

AF:

0.0531

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.0140

Gnomad EAS exome

AF:

0.00375

Gnomad SAS exome

AF:

0.0201

Gnomad FIN exome

AF:

0.00610

Gnomad NFE exome

AF:

0.0114

Gnomad OTH exome

AF:

0.0158

GnomAD4 exome

AF:

0.0117

AC:

17047

AN:

1461102

Hom.:

166

Cov.:

AF XY:

0.0120

AC XY:

8752

AN XY:

726862

show subpopulations

Gnomad4 AFR exome

AF:

0.0511

Gnomad4 AMR exome

AF:

0.0118

Gnomad4 ASJ exome

AF:

0.0133

Gnomad4 EAS exome

AF:

0.00489

Gnomad4 SAS exome

AF:

0.0204

Gnomad4 FIN exome

AF:

0.00661

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.0138

GnomAD4 genome

AF:

0.0223

AC:

3393

AN:

151964

Hom.:

Cov.:

AF XY:

0.0225

AC XY:

1669

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.0498

Gnomad4 AMR

AF:

0.0214

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.00349

Gnomad4 SAS

AF:

0.0195

Gnomad4 FIN

AF:

0.00481

Gnomad4 NFE

AF:

0.0108

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0179

Hom.:

Bravo

AF:

0.0248

TwinsUK

AF:

0.00890

AC:

ALSPAC

AF:

0.00934

AC:

ESP6500AA

AF:

0.0515

AC:

227

ESP6500EA

AF:

0.0105

AC:

ExAC

AF:

0.0155

AC:

1886

Asia WGS

AF:

0.0130

AC:

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.0128

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Agammaglobulinemia 2, autosomal recessive

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 20, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.60

CADD

Benign

8.8

DANN

Benign

0.67

DEOGEN2

Benign

0.30

T;.

Eigen

Benign

-0.85

Eigen_PC

Benign

-0.97

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.83

T;T

MetaRNN

Benign

0.0039

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.7

L;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.41

PROVEAN

Pathogenic

-6.3

D;D

REVEL

Benign

0.074

Sift

Uncertain

0.015

D;D

Sift4G

Uncertain

0.011

D;.

Polyphen

0.084

B;.

Vest4

0.051

MPC

0.064

ClinPred

0.017

GERP RS

1.3

Varity_R

0.29

gMVP

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over