1-160488820-A-G

Variant names:

• chr1-160488820-A-G
• rs1041068
• NM_001184714.2:c.879+268T>C

Variant summary

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

The NM_001184714.2(SLAMF6):​c.879+268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,080 control chromosomes in the GnomAD database, including 37,514 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 0.70 (37514 hom., cov: 31)
• Consequence: SLAMF6 NM_001184714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 4 publications found

Genes affected

SLAMF6 (HGNC:21392): (SLAM family member 6) The protein encoded by this gene is a type I transmembrane protein, belonging to the CD2 subfamily of the immunoglobulin superfamily. This encoded protein is expressed on Natural killer (NK), T, and B lymphocytes. It undergoes tyrosine phosphorylation and associates with the Src homology 2 domain-containing protein (SH2D1A) as well as with SH2 domain-containing phosphatases (SHPs). It functions as a coreceptor in the process of NK cell activation. It can also mediate inhibitory signals in NK cells from X-linked lymphoproliferative patients. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184714.2. 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
	SLAMF6	NM_001184714.2	MANE Select	c.879+268T>C		intron	N/A	NP_001171643.1
	SLAMF6	NM_052931.5		c.876+268T>C		intron	N/A	NP_443163.1
	SLAMF6	NM_001184715.2		c.729+268T>C		intron	N/A	NP_001171644.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF6	ENST00000368057.8	TSL:1 MANE Select	c.879+268T>C		intron	N/A	ENSP00000357036.3
	SLAMF6	ENST00000368059.7	TSL:1	c.876+268T>C		intron	N/A	ENSP00000357038.3
	SLAMF6	ENST00000368055.1	TSL:2	c.546+268T>C		intron	N/A	ENSP00000357034.1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106560 AN: 151962 Hom.: 37480 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.701 AC: 106643 AN: 152080 Hom.: 37514 Cov.: 31 AF XY: 0.701 AC XY: 52091 AN XY: 74322

African (AFR) AF: 0.696 AC: 28872 AN: 41470

American (AMR) AF: 0.641 AC: 9794 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3391 AN: 5164

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4822

European-Finnish (FIN) AF: 0.706 AC: 7465 AN: 10576

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.709 AC: 48227 AN: 67982

Other (OTH) AF: 0.721 AC: 1525 AN: 2116

Alfa AF: 0.694 Hom.: 18483

Bravo AF: 0.695

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		2.0
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: rs1041068; hg19: chr1-160458610;