Variant 1-160646913-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003037.5(SLAMF1):c.33C>A(p.Phe11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,599,616 control chromosomes in the GnomAD database, including 29,962 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.15 ( 2115 hom., cov: 32)

Exomes 𝑓: 0.19 ( 27847 hom. )

Consequence

SLAMF1
NM_003037.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.144

Variant links:

Genes affected

SLAMF1 (HGNC:10903): (signaling lymphocytic activation molecule family member 1) Enables SH2 domain binding activity and identical protein binding activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SLAMF1 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=0.009170055).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAMF1	NM_003037.5 linkuse as main transcript	c.33C>A	p.Phe11Leu	missense_variant	1/7	ENST00000302035.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF1	ENST00000302035.11 linkuse as main transcript	c.33C>A	p.Phe11Leu	missense_variant	1/7	1	NM_003037.5	P1	Q13291-1
SLAMF1	ENST00000538290.2 linkuse as main transcript	c.33C>A	p.Phe11Leu	missense_variant	1/8	1			Q13291-4
SLAMF1	ENST00000494463.1 linkuse as main transcript	n.109C>A		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22076

AN:

152016

Hom.:

2113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0398

Gnomad AMI

AF:

0.250

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0423

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.169

AC:

41871

AN:

248184

Hom.:

4180

AF XY:

0.167

AC XY:

22425

AN XY:

134086

show subpopulations

Gnomad AFR exome

AF:

0.0314

Gnomad AMR exome

AF:

0.282

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.0428

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.142

Gnomad NFE exome

AF:

0.197

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.189

AC:

273000

AN:

1447482

Hom.:

27847

Cov.:

AF XY:

0.187

AC XY:

134482

AN XY:

720724

show subpopulations

Gnomad4 AFR exome

AF:

0.0309

Gnomad4 AMR exome

AF:

0.270

Gnomad4 ASJ exome

AF:

0.146

Gnomad4 EAS exome

AF:

0.0504

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.205

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.145

AC:

22077

AN:

152134

Hom.:

2115

Cov.:

AF XY:

0.143

AC XY:

10626

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0397

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.0422

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.184

Hom.:

6573

Bravo

AF:

0.149

TwinsUK

AF:

0.210

AC:

778

ALSPAC

AF:

0.212

AC:

816

ESP6500AA

AF:

0.0359

AC:

158

ESP6500EA

AF:

0.203

AC:

1748

ExAC

AF:

0.162

AC:

19703

Asia WGS

AF:

0.0790

AC:

274

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.97

DANN

Benign

0.55

DEOGEN2

Benign

0.042

T;.;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.54

T;T;T

MetaRNN

Benign

0.0092

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.12

N;.;N

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

0.36

N;N;N

REVEL

Benign

0.013

Sift

Benign

0.67

T;T;T

Sift4G

Benign

0.78

T;T;T

Polyphen

0.0020

B;.;.

Vest4

0.0070

MutPred

0.46

Gain of disorder (P = 0.163);Gain of disorder (P = 0.163);Gain of disorder (P = 0.163);

MPC

0.24

ClinPred

0.00044

GERP RS

0.79

Varity_R

0.033

gMVP

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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