Variant 17-16443931-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001113567.3(LRRC75A):c.692G>A(p.Arg231His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00251 in 1,613,034 control chromosomes in the GnomAD database, including 148 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0044 ( 25 hom., cov: 33)

Exomes 𝑓: 0.0023 ( 123 hom. )

Consequence

LRRC75A
NM_001113567.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.49

Variant links:

Genes affected

LRRC75A (HGNC:32403): (leucine rich repeat containing 75A) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LRRC75A links:

SNHG29 (HGNC:28619): (small nucleolar RNA host gene 29)

SNHG29 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=0.004951209).

BP6

Variant 17-16443931-C-T is Benign according to our data. Variant chr17-16443931-C-T is described in ClinVar as [Benign]. Clinvar id is 788905.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC75A	NM_001113567.3 linkuse as main transcript	c.692G>A	p.Arg231His	missense_variant	4/4	ENST00000470794.2
SNHG29	NR_027171.1 linkuse as main transcript	n.554+2801C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC75A	ENST00000470794.2 linkuse as main transcript	c.692G>A	p.Arg231His	missense_variant	4/4	1	NM_001113567.3	P1	Q8NAA5-1
SNHG29	ENST00000702366.1 linkuse as main transcript	n.238+2801C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00440

AC:

669

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0340

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00810

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000206

Gnomad OTH

AF:

0.00622

GnomAD3 exomes

AF:

0.00915

AC:

2287

AN:

250078

Hom.:

AF XY:

0.00719

AC XY:

972

AN XY:

135256

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.0586

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000360

Gnomad FIN exome

AF:

0.00936

Gnomad NFE exome

AF:

0.0000972

Gnomad OTH exome

AF:

0.00605

GnomAD4 exome

AF:

0.00231

AC:

3371

AN:

1460720

Hom.:

123

Cov.:

AF XY:

0.00205

AC XY:

1489

AN XY:

726674

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.0595

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000394

Gnomad4 FIN exome

AF:

0.00897

Gnomad4 NFE exome

AF:

0.0000522

Gnomad4 OTH exome

AF:

0.00205

GnomAD4 genome

AF:

0.00444

AC:

676

AN:

152314

Hom.:

Cov.:

AF XY:

0.00510

AC XY:

380

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.0344

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00810

Gnomad4 NFE

AF:

0.000206

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.000597

Hom.:

Bravo

AF:

0.00671

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00685

AC:

832

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

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

Dec 20, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.028

Eigen

Benign

-0.035

Eigen_PC

Benign

0.12

FATHMM_MKL

Benign

0.36

LIST_S2

Uncertain

0.93

MetaRNN

Benign

0.0050

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.98

D;D

PrimateAI

Benign

0.35

PROVEAN

Benign

-2.2

REVEL

Benign

0.041

Sift

Benign

0.18

Sift4G

Benign

0.37

Polyphen

0.064

Vest4

0.091

MVP

0.043

MPC

0.62

ClinPred

0.012

GERP RS

4.3

Varity_R

0.091

gMVP

0.25

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