rs10494344

chr1-160502550-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001184714.2(SLAMF6):c.50-6157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,178 control chromosomes in the GnomAD database, including 1,721 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 0.091 (1721 hom., cov: 32)
• Consequence: SLAMF6 NM_001184714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAMF6	NM_001184714.2	c.50-6157T>C		intron_variant		ENST00000368057.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF6	ENST00000368057.8	c.50-6157T>C		intron_variant		1	NM_001184714.2	A2
SLAMF6	ENST00000368059.7	c.50-6157T>C		intron_variant		1		P4
SLAMF6	ENST00000368055.1	c.50-11162T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13853 AN: 152060 Hom.: 1711 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.00649

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00867

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0914 AC: 13904 AN: 152178 Hom.: 1721 Cov.: 32 AF XY: 0.0911 AC XY: 6782 AN XY: 74416

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0421

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.00649

Gnomad4 NFE AF: 0.00868

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0282 Hom.: 359

Bravo AF: 0.0991

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.2
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494344; hg19: chr1-160472340;