chr1-160495121-C-A

Position:

• chr1-160495121-C-A

Variant summary

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

The NM_001184714.2(SLAMF6):​c.382+940G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,288 control chromosomes in the GnomAD database, including 69,445 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 0.95 (69445 hom., cov: 32)
• Consequence: SLAMF6 NM_001184714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAMF6	NM_001184714.2	c.382+940G>T		intron_variant		ENST00000368057.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF6	ENST00000368057.8	c.382+940G>T		intron_variant		1	NM_001184714.2	A2
SLAMF6	ENST00000368059.7	c.382+940G>T		intron_variant		1		P4
SLAMF6	ENST00000368055.1	c.50-3733G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145258 AN: 152170 Hom.: 69381 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.955 AC: 145381 AN: 152288 Hom.: 69445 Cov.: 32 AF XY: 0.953 AC XY: 70972 AN XY: 74456

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.970

Alfa AF: 0.943 Hom.: 44844

Bravo AF: 0.959

Asia WGS AF: 0.911 AC: 3166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.5
DANN	Benign	0.71

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: rs1265883; hg19: chr1-160464911;