Genetic Variant SAMM50:p.Gly137Gly (chr22-43972324-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_015380.5(SAMM50):c.411A>G(p.Gly137Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 1,588,460 control chromosomes in the GnomAD database, including 230,729 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26765 hom., cov: 32)

Exomes 𝑓: 0.53 ( 203964 hom. )

Consequence

SAMM50
NM_015380.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.553

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 22-43972324-A-G is Benign according to our data. Variant chr22-43972324-A-G is described in ClinVar as [Benign]. Clinvar id is 1283359.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.553 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMM50	NM_015380.5 link	c.411A>G	p.Gly137Gly	synonymous_variant	Exon 5 of 15	ENST00000350028.5	NP_056195.3	Q9Y512

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMM50	ENST00000350028.5 link	c.411A>G	p.Gly137Gly	synonymous_variant	Exon 5 of 15	1	NM_015380.5	ENSP00000345445.4		Q9Y512
SAMM50	ENST00000493161.1 link	n.593A>G		non_coding_transcript_exon_variant	Exon 5 of 7	3

Frequencies

GnomAD3 genomes

AF:

0.584

AC:

88798

AN:

151924

Hom.:

26717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.509

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.699

Gnomad FIN

AF:

0.608

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.499

Gnomad OTH

AF:

0.525

GnomAD3 exomes

AF:

0.572

AC:

136052

AN:

237666

Hom.:

40437

AF XY:

0.571

AC XY:

73387

AN XY:

128634

show subpopulations

Gnomad AFR exome

AF:

0.716

Gnomad AMR exome

AF:

0.538

Gnomad ASJ exome

AF:

0.450

Gnomad EAS exome

AF:

0.829

Gnomad SAS exome

AF:

0.690

Gnomad FIN exome

AF:

0.603

Gnomad NFE exome

AF:

0.500

Gnomad OTH exome

AF:

0.521

GnomAD4 exome

AF:

0.526

AC:

755054

AN:

1436420

Hom.:

203964

Cov.:

AF XY:

0.530

AC XY:

378519

AN XY:

714690

show subpopulations

Gnomad4 AFR exome

AF:

0.713

Gnomad4 AMR exome

AF:

0.535

Gnomad4 ASJ exome

AF:

0.447

Gnomad4 EAS exome

AF:

0.850

Gnomad4 SAS exome

AF:

0.685

Gnomad4 FIN exome

AF:

0.610

Gnomad4 NFE exome

AF:

0.494

Gnomad4 OTH exome

AF:

0.537

GnomAD4 genome

AF:

0.585

AC:

88897

AN:

152040

Hom.:

26765

Cov.:

AF XY:

0.590

AC XY:

43856

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.711

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.697

Gnomad4 FIN

AF:

0.608

Gnomad4 NFE

AF:

0.499

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.515

Hom.:

47673

Bravo

AF:

0.584

Asia WGS

AF:

0.758

AC:

2637

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 26, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

5.1

DANN

Benign

0.79

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