Variant rs3761472 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015380.5(SAMM50):c.329A>G(p.Asp110Gly) variant causes a missense change. The variant allele was found at a frequency of 0.172 in 1,561,102 control chromosomes in the GnomAD database, including 25,689 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.19 ( 2921 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22768 hom. )

Consequence

SAMM50
NM_015380.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.66

Variant links:

Genes affected

SAMM50 (HGNC:24276): (SAMM50 sorting and assembly machinery component) This gene encodes a component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The Sam complex functions in the assembly of beta-barrel proteins into the outer mitochondrial membrane.[provided by RefSeq, Jun 2011]

SAMM50 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026952326).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMM50	NM_015380.5 linkuse as main transcript	c.329A>G	p.Asp110Gly	missense_variant	5/15	ENST00000350028.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMM50	ENST00000350028.5 linkuse as main transcript	c.329A>G	p.Asp110Gly	missense_variant	5/15	1	NM_015380.5	P1
SAMM50	ENST00000493161.1 linkuse as main transcript	n.511A>G		non_coding_transcript_exon_variant	5/7	3

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28574

AN:

151974

Hom.:

2917

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.207

AC:

46333

AN:

223714

Hom.:

5623

AF XY:

0.202

AC XY:

24569

AN XY:

121430

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.386

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.167

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.171

AC:

240419

AN:

1409010

Hom.:

22768

Cov.:

AF XY:

0.172

AC XY:

120125

AN XY:

700424

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.300

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.401

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.188

AC:

28585

AN:

152092

Hom.:

2921

Cov.:

AF XY:

0.194

AC XY:

14407

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.170

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.130

Gnomad4 EAS

AF:

0.385

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.187

Alfa

AF:

0.171

Hom.:

6107

Bravo

AF:

0.192

TwinsUK

AF:

0.157

AC:

584

ALSPAC

AF:

0.167

AC:

642

ESP6500AA

AF:

0.178

AC:

786

ESP6500EA

AF:

0.156

AC:

1339

ExAC

AF:

0.207

AC:

25125

Asia WGS

AF:

0.270

AC:

936

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.042

Eigen

Benign

-0.045

Eigen_PC

Benign

0.094

FATHMM_MKL

Uncertain

0.93

LIST_S2

Uncertain

0.87

MetaRNN

Benign

0.0027

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.7

MutationTaster

Benign

6.5e-9

P;P

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-1.2

REVEL

Benign

0.080

Sift

Benign

0.21

Sift4G

Benign

0.11

Polyphen

0.010

Vest4

0.080

MPC

0.36

ClinPred

0.019

GERP RS

4.8

Varity_R

0.23

gMVP

0.54

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over