Variant 11-62422264-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_003357.5(SCGB1A1):c.99C>T(p.Thr33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00579 in 1,613,622 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0059 ( 40 hom. )

Consequence

SCGB1A1
NM_003357.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.611

Variant links:

Genes affected

SCGB1A1 (HGNC:12523): (secretoglobin family 1A member 1) This gene encodes a member of the secretoglobin family of small secreted proteins. The encoded protein has been implicated in numerous functions including anti-inflammation, inhibition of phospholipase A2 and the sequestering of hydrophobic ligands. Defects in this gene are associated with a susceptibility to asthma. [provided by RefSeq, May 2010]

SCGB1A1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-62422264-C-T is Benign according to our data. Variant chr11-62422264-C-T is described in ClinVar as [Benign]. Clinvar id is 791050.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.611 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1A1	NM_003357.5 linkuse as main transcript	c.99C>T	p.Thr33=	synonymous_variant	2/3	ENST00000278282.3
LOC102723765	XR_007062699.1 linkuse as main transcript	n.237+4423G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
SCGB1A1	ENST00000278282.3 linkuse as main transcript	c.99C>T	p.Thr33=	synonymous_variant	2/3	1	NM_003357.5	P1
	ENST00000528983.1 linkuse as main transcript	n.91G>A		non_coding_transcript_exon_variant	2/2	3
SCGB1A1	ENST00000534397.5 linkuse as main transcript	c.-7C>T		5_prime_UTR_variant	3/4	3

Frequencies

GnomAD3 genomes

AF:

0.00458

AC:

697

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00236

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00538

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00800

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00412

AC:

1034

AN:

251074

Hom.:

AF XY:

0.00416

AC XY:

564

AN XY:

135668

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00154

Gnomad ASJ exome

AF:

0.0000994

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000621

Gnomad FIN exome

AF:

0.00707

Gnomad NFE exome

AF:

0.00676

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00592

AC:

8653

AN:

1461326

Hom.:

Cov.:

AF XY:

0.00575

AC XY:

4181

AN XY:

726936

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000754

Gnomad4 FIN exome

AF:

0.00594

Gnomad4 NFE exome

AF:

0.00703

Gnomad4 OTH exome

AF:

0.00576

GnomAD4 genome

AF:

0.00458

AC:

697

AN:

152296

Hom.:

Cov.:

AF XY:

0.00435

AC XY:

324

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00538

Gnomad4 NFE

AF:

0.00800

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00622

Hom.:

Bravo

AF:

0.00386

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00655

EpiControl

AF:

0.00593

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.1

DANN

Benign

0.46

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