Variant 7-93135669-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_152703.5(SAMD9L):c.303G>A(p.Gln101Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,613,698 control chromosomes in the GnomAD database, including 36,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 9123 hom., cov: 32)

Exomes 𝑓: 0.16 ( 26994 hom. )

Consequence

SAMD9L
NM_152703.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.48

Variant links:

Genes affected

SAMD9L (HGNC:1349): (sterile alpha motif domain containing 9 like) This gene encodes a cytoplasmic protein that acts as a tumor suppressor but also plays a key role in cell proliferation and the innate immune response to viral infection. The encoded protein contains an N-terminal sterile alpha motif domain. Naturally occurring mutations in this gene are associated with myeloid disorders such as juvenile myelomonocytic leukemia, acute myeloid leukemia, and myelodysplastic syndrome. Naturally occurring mutations are also associated with hepatitis-B related hepatocellular carcinoma, normophosphatemic familial tumoral calcinosis, and ataxia-pancytopenia syndrome. [provided by RefSeq, Apr 2017]

SAMD9L 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=-0.93).

BP6

Variant 7-93135669-C-T is Benign according to our data. Variant chr7-93135669-C-T is described in ClinVar as [Benign]. Clinvar id is 1170232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD9L	NM_152703.5 linkuse as main transcript	c.303G>A	p.Gln101Gln	synonymous_variant	5/5	ENST00000318238.9	NP_689916.2	Q8IVG5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD9L	ENST00000318238.9 linkuse as main transcript	c.303G>A	p.Gln101Gln	synonymous_variant	5/5	1	NM_152703.5	ENSP00000326247.4		Q8IVG5-1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42345

AN:

151878

Hom.:

9090

Cov.:

show subpopulations

Gnomad AFR

AF:

0.567

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.0874

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0949

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.238

GnomAD3 exomes

AF:

0.225

AC:

56455

AN:

250940

Hom.:

10459

AF XY:

0.203

AC XY:

27494

AN XY:

135618

show subpopulations

Gnomad AFR exome

AF:

0.573

Gnomad AMR exome

AF:

0.428

Gnomad ASJ exome

AF:

0.0829

Gnomad EAS exome

AF:

0.575

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.0991

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.185

GnomAD4 exome

AF:

0.158

AC:

230418

AN:

1461702

Hom.:

26994

Cov.:

AF XY:

0.153

AC XY:

111495

AN XY:

727144

show subpopulations

Gnomad4 AFR exome

AF:

0.570

Gnomad4 AMR exome

AF:

0.416

Gnomad4 ASJ exome

AF:

0.0826

Gnomad4 EAS exome

AF:

0.547

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.179

GnomAD4 genome

AF:

0.279

AC:

42444

AN:

151996

Hom.:

9123

Cov.:

AF XY:

0.278

AC XY:

20625

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.567

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.0874

Gnomad4 EAS

AF:

0.568

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.0949

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.244

Alfa

AF:

0.151

Hom.:

3821

Bravo

AF:

0.313

Asia WGS

AF:

0.359

AC:

1247

AN:

3476

EpiCase

AF:

0.125

EpiControl

AF:

0.119

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 13, 2023	- -

SAMD9L-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 09, 2023

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.28

DANN

Benign

0.30

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