rs2753260

Variant names:

• chr1-160618805-C-A
• rs2753260
• NM_003037.5:c.864+971G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-160618805-C-A
• chr1-160618805-C-G
• chr1-160618805-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003037.5(SLAMF1):​c.864+971G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,060 control chromosomes in the GnomAD database, including 45,502 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 0.77 (45502 hom., cov: 31)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	NM_003037.5	MANE Select	c.864+971G>T		intron	N/A	NP_003028.1
	SLAMF1	NM_001330754.2		c.947+971G>T		intron	N/A	NP_001317683.1
	SLAMF1	NR_104399.3		n.889+5291G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	ENST00000302035.11	TSL:1 MANE Select	c.864+971G>T		intron	N/A	ENSP00000306190.6
	SLAMF1	ENST00000538290.2	TSL:1	c.947+971G>T		intron	N/A	ENSP00000438406.2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116877 AN: 151942 Hom.: 45451 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.734

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 116989 AN: 152060 Hom.: 45502 Cov.: 31 AF XY: 0.777 AC XY: 57781 AN XY: 74330

African (AFR) AF: 0.863 AC: 35800 AN: 41460

American (AMR) AF: 0.774 AC: 11833 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2548 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4428 AN: 5172

South Asian (SAS) AF: 0.836 AC: 4030 AN: 4820

European-Finnish (FIN) AF: 0.805 AC: 8522 AN: 10588

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47426 AN: 67952

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.718 Hom.: 72354

Bravo AF: 0.769

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.018
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: rs2753260; hg19: chr1-160588595;