Variant chr22-43972861-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_015380.5(SAMM50):c.430-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 1,539,410 control chromosomes in the GnomAD database, including 180,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26107 hom., cov: 31)

Exomes 𝑓: 0.49 ( 154253 hom. )

Consequence

SAMM50
NM_015380.5 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001562

Clinical Significance

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

Conservation

PhyloP100: -0.596

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 22-43972861-C-T is Benign according to our data. Variant chr22-43972861-C-T is described in ClinVar as [Benign]. Clinvar id is 769164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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.430-10C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000350028.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMM50	ENST00000350028.5 linkuse as main transcript	c.430-10C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_015380.5	P1
SAMM50	ENST00000493161.1 linkuse as main transcript	n.612-10C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

87338

AN:

150120

Hom.:

26062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.709

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.432

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.526

GnomAD3 exomes

AF:

0.506

AC:

103392

AN:

204356

Hom.:

22253

AF XY:

0.502

AC XY:

56059

AN XY:

111780

show subpopulations

Gnomad AFR exome

AF:

0.673

Gnomad AMR exome

AF:

0.480

Gnomad ASJ exome

AF:

0.408

Gnomad EAS exome

AF:

0.707

Gnomad SAS exome

AF:

0.601

Gnomad FIN exome

AF:

0.546

Gnomad NFE exome

AF:

0.440

Gnomad OTH exome

AF:

0.470

GnomAD4 exome

AF:

0.491

AC:

681980

AN:

1389184

Hom.:

154253

Cov.:

AF XY:

0.494

AC XY:

341534

AN XY:

691296

show subpopulations

Gnomad4 AFR exome

AF:

0.692

Gnomad4 AMR exome

AF:

0.504

Gnomad4 ASJ exome

AF:

0.423

Gnomad4 EAS exome

AF:

0.771

Gnomad4 SAS exome

AF:

0.632

Gnomad4 FIN exome

AF:

0.572

Gnomad4 NFE exome

AF:

0.463

Gnomad4 OTH exome

AF:

0.504

GnomAD4 genome

AF:

0.582

AC:

87432

AN:

150226

Hom.:

26107

Cov.:

AF XY:

0.587

AC XY:

43057

AN XY:

73298

show subpopulations

Gnomad4 AFR

AF:

0.710

Gnomad4 AMR

AF:

0.529

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.696

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.496

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.524

Hom.:

11085

Bravo

AF:

0.582

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000016

dbscSNV1_RF

Benign

0.0020

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