rs164288

Variant names:

• chr1-160634683-G-A
• rs164288
• NM_003037.5:c.630C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_003037.5(SLAMF1):​c.630C>T​(p.Thr210Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 1,613,984 control chromosomes in the GnomAD database, including 5,754 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.

• Frequency:
  • Genomes: 𝑓 0.065 (389 hom., cov: 32)
  • Exomes 𝑓: 0.083 (5365 hom.)
• Consequence: SLAMF1 NM_003037.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37
• Publications: 22 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP7: Synonymous conserved (PhyloP=-3.37 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.630C>T	p.Thr210Thr	synonymous_variant	Exon 3 of 7	ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.630C>T	p.Thr210Thr	synonymous_variant	Exon 3 of 7	1	NM_003037.5	ENSP00000306190.6
SLAMF1	ENST00000538290.2	c.630C>T	p.Thr210Thr	synonymous_variant	Exon 3 of 8	1		ENSP00000438406.2

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 9949 AN: 152044 Hom.: 388 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0738

GnomAD2 exomes AF: 0.0725 AC: 18217 AN: 251284 AF XY: 0.0743

Gnomad AFR exome AF: 0.0267

Gnomad AMR exome AF: 0.0447

Gnomad ASJ exome AF: 0.139

Gnomad EAS exome AF: 0.00663

Gnomad FIN exome AF: 0.0662

Gnomad NFE exome AF: 0.0946

Gnomad OTH exome AF: 0.0849

GnomAD4 exome AF: 0.0827 AC: 120894 AN: 1461822 Hom.: 5365 Cov.: 32 AF XY: 0.0825 AC XY: 60031 AN XY: 727214

African (AFR) AF: 0.0245 AC: 819 AN: 33480

American (AMR) AF: 0.0468 AC: 2093 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 3750 AN: 26136

East Asian (EAS) AF: 0.0157 AC: 622 AN: 39698

South Asian (SAS) AF: 0.0679 AC: 5860 AN: 86252

European-Finnish (FIN) AF: 0.0697 AC: 3725 AN: 53418

Middle Eastern (MID) AF: 0.105 AC: 603 AN: 5768

European-Non Finnish (NFE) AF: 0.0885 AC: 98426 AN: 1111952

Other (OTH) AF: 0.0827 AC: 4996 AN: 60394

GnomAD4 genome AF: 0.0654 AC: 9954 AN: 152162 Hom.: 389 Cov.: 32 AF XY: 0.0638 AC XY: 4745 AN XY: 74380

African (AFR) AF: 0.0301 AC: 1248 AN: 41526

American (AMR) AF: 0.0597 AC: 913 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5186

South Asian (SAS) AF: 0.0591 AC: 284 AN: 4808

European-Finnish (FIN) AF: 0.0656 AC: 694 AN: 10574

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0884 AC: 6007 AN: 67990

Other (OTH) AF: 0.0731 AC: 154 AN: 2108

Alfa AF: 0.0843 Hom.: 946

Bravo AF: 0.0651

Asia WGS AF: 0.0400 AC: 140 AN: 3478

EpiCase AF: 0.0934

EpiControl AF: 0.0931

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.34
DANN	Benign	0.63
PhyloP100		-3.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs164288; hg19: chr1-160604473; COSMIC: COSV52500994; COSMIC: COSV52500994;