dbSNP rs62073222: LRRC37A:p.Pro737Pro (chr17-46297344-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014834.4(LRRC37A):c.2211A>G(p.Pro737Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 1,135,268 control chromosomes in the GnomAD database, including 324,502 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 23199 hom., cov: 18)

Exomes 𝑓: 0.70 ( 324502 hom. )

Failed GnomAD Quality Control

Consequence

LRRC37A
NM_014834.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.18

Variant links:

Genes affected

LRRC37A (HGNC:29069): (leucine rich repeat containing 37A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRRC37A links:

ARL17B (HGNC:32387): (ADP ribosylation factor like GTPase 17B) Predicted to enable GTP binding activity. Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Predicted to be located in Golgi apparatus. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARL17B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 17-46297344-A-G is Benign according to our data. Variant chr17-46297344-A-G is described in ClinVar as [Benign]. Clinvar id is 403059.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.18 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A	NM_014834.4 link	c.2211A>G	p.Pro737Pro	synonymous_variant	Exon 1 of 14	ENST00000320254.5	NP_055649.4	A6NMS7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC37A	ENST00000320254.5 link	c.2211A>G	p.Pro737Pro	synonymous_variant	Exon 1 of 14	1	NM_014834.4	ENSP00000326324.5		A6NMS7

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

65820

AN:

111500

Hom.:

23198

Cov.:

FAILED QC

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.662

Gnomad EAS

AF:

0.950

Gnomad SAS

AF:

0.885

Gnomad FIN

AF:

0.852

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.687

Gnomad OTH

AF:

0.585

GnomAD3 exomes

AF:

0.740

AC:

41848

AN:

56530

Hom.:

17748

AF XY:

0.749

AC XY:

21287

AN XY:

28430

show subpopulations

Gnomad AFR exome

AF:

0.344

Gnomad AMR exome

AF:

0.713

Gnomad ASJ exome

AF:

0.699

Gnomad EAS exome

AF:

0.981

Gnomad SAS exome

AF:

0.915

Gnomad FIN exome

AF:

0.868

Gnomad NFE exome

AF:

0.713

Gnomad OTH exome

AF:

0.697

GnomAD4 exome

AF:

0.700

AC:

794229

AN:

1135268

Hom.:

324502

Cov.:

AF XY:

0.710

AC XY:

407664

AN XY:

574036

show subpopulations

Gnomad4 AFR exome

AF:

0.345

Gnomad4 AMR exome

AF:

0.714

Gnomad4 ASJ exome

AF:

0.668

Gnomad4 EAS exome

AF:

0.979

Gnomad4 SAS exome

AF:

0.895

Gnomad4 FIN exome

AF:

0.885

Gnomad4 NFE exome

AF:

0.678

Gnomad4 OTH exome

AF:

0.695

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.590

AC:

65831

AN:

111574

Hom.:

23199

Cov.:

AF XY:

0.598

AC XY:

31767

AN XY:

53120

show subpopulations

Gnomad4 AFR

AF:

0.338

Gnomad4 AMR

AF:

0.581

Gnomad4 ASJ

AF:

0.662

Gnomad4 EAS

AF:

0.950

Gnomad4 SAS

AF:

0.886

Gnomad4 FIN

AF:

0.852

Gnomad4 NFE

AF:

0.687

Gnomad4 OTH

AF:

0.589

Alfa

AF:

0.602

Hom.:

2501

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.6

DANN

Benign

0.34

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