Variant chr1-160610759-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.997C>A(p.Pro333Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0803 in 1,611,012 control chromosomes in the GnomAD database, including 5,787 homozygotes. In-silico tool predicts 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 0.061 ( 380 hom., cov: 33)

Exomes 𝑓: 0.082 ( 5407 hom. )

Consequence

SLAMF1
NM_003037.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.69

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=0.0018964708).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 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.997C>A	p.Pro333Thr	missense_variant	7/7	ENST00000302035.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF1	ENST00000302035.11 linkuse as main transcript	c.997C>A	p.Pro333Thr	missense_variant	7/7	1	NM_003037.5	P1	Q13291-1
SLAMF1	ENST00000538290.2 linkuse as main transcript			downstream_gene_variant		1			Q13291-4

Frequencies

GnomAD3 genomes

AF:

0.0615

AC:

9363

AN:

152186

Hom.:

382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0155

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.00365

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.0666

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0895

Gnomad OTH

AF:

0.0757

GnomAD3 exomes

AF:

0.0699

AC:

17536

AN:

251018

Hom.:

819

AF XY:

0.0713

AC XY:

9669

AN XY:

135650

show subpopulations

Gnomad AFR exome

AF:

0.0129

Gnomad AMR exome

AF:

0.0430

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.000871

Gnomad SAS exome

AF:

0.0575

Gnomad FIN exome

AF:

0.0675

Gnomad NFE exome

AF:

0.0961

Gnomad OTH exome

AF:

0.0818

GnomAD4 exome

AF:

0.0822

AC:

119946

AN:

1458708

Hom.:

5407

Cov.:

AF XY:

0.0819

AC XY:

59451

AN XY:

725792

show subpopulations

Gnomad4 AFR exome

AF:

0.0112

Gnomad4 AMR exome

AF:

0.0452

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.00774

Gnomad4 SAS exome

AF:

0.0593

Gnomad4 FIN exome

AF:

0.0713

Gnomad4 NFE exome

AF:

0.0901

Gnomad4 OTH exome

AF:

0.0783

GnomAD4 genome

AF:

0.0614

AC:

9355

AN:

152304

Hom.:

380

Cov.:

AF XY:

0.0607

AC XY:

4519

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0154

Gnomad4 AMR

AF:

0.0616

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.00366

Gnomad4 SAS

AF:

0.0543

Gnomad4 FIN

AF:

0.0666

Gnomad4 NFE

AF:

0.0895

Gnomad4 OTH

AF:

0.0750

Alfa

AF:

0.0868

Hom.:

1525

Bravo

AF:

0.0606

ESP6500AA

AF:

0.0175

AC:

ESP6500EA

AF:

0.0888

AC:

764

ExAC

AF:

0.0719

AC:

8731

Asia WGS

AF:

0.0290

AC:

102

AN:

3478

EpiCase

AF:

0.0927

EpiControl

AF:

0.0939

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.46

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.23

Eigen

Uncertain

0.53

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.81

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

MutationTaster

Benign

0.99

D;D;D

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-2.2

REVEL

Benign

0.25

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.16

MPC

0.84

ClinPred

0.029

GERP RS

4.1

Varity_R

0.25

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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