Variant 11-35432617-A-G 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_001001991.3(PAMR1):c.1902T>C(p.His634=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00648 in 1,614,086 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0067 ( 32 hom. )

Consequence

PAMR1
NM_001001991.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00200

Variant links:

Genes affected

PAMR1 (HGNC:24554): (peptidase domain containing associated with muscle regeneration 1) Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PAMR1 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=-0.56).

BP6

Variant 11-35432617-A-G is Benign according to our data. Variant chr11-35432617-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2641723.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.002 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PAMR1	NM_001001991.3 linkuse as main transcript	c.1902T>C	p.His634=	synonymous_variant	11/11	ENST00000619888.5
PAMR1	NM_015430.4 linkuse as main transcript	c.1953T>C	p.His651=	synonymous_variant	12/12
PAMR1	NM_001282675.2 linkuse as main transcript	c.1782T>C	p.His594=	synonymous_variant	13/13
PAMR1	NM_001282676.2 linkuse as main transcript	c.1569T>C	p.His523=	synonymous_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAMR1	ENST00000619888.5 linkuse as main transcript	c.1902T>C	p.His634=	synonymous_variant	11/11	1	NM_001001991.3	P1	Q6UXH9-1

Frequencies

GnomAD3 genomes

AF:

0.00474

AC:

722

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00763

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00817

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00511

AC:

1281

AN:

250788

Hom.:

AF XY:

0.00500

AC XY:

677

AN XY:

135526

show subpopulations

Gnomad AFR exome

AF:

0.000864

Gnomad AMR exome

AF:

0.000956

Gnomad ASJ exome

AF:

0.00248

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000491

Gnomad FIN exome

AF:

0.00991

Gnomad NFE exome

AF:

0.00819

Gnomad OTH exome

AF:

0.00848

GnomAD4 exome

AF:

0.00666

AC:

9740

AN:

1461770

Hom.:

Cov.:

AF XY:

0.00653

AC XY:

4746

AN XY:

727152

show subpopulations

Gnomad4 AFR exome

AF:

0.000956

Gnomad4 AMR exome

AF:

0.00105

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.000499

Gnomad4 FIN exome

AF:

0.0113

Gnomad4 NFE exome

AF:

0.00772

Gnomad4 OTH exome

AF:

0.00571

GnomAD4 genome

AF:

0.00474

AC:

722

AN:

152316

Hom.:

Cov.:

AF XY:

0.00450

AC XY:

335

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00763

Gnomad4 NFE

AF:

0.00817

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00679

Hom.:

Bravo

AF:

0.00401

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00682

EpiControl

AF:

0.00605

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

PAMR1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.33

DANN

Benign

0.58

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