rs489286

Variant names:

• chr1-160752760-A-C
• rs489286
• NM_021181.5:c.937-346A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-160752760-A-C
• chr1-160752760-A-G
• chr1-160752760-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021181.5(SLAMF7):​c.937-346A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: SLAMF7 NM_021181.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 21 publications found

Genes affected

SLAMF7 (HGNC:21394): (SLAM family member 7) Enables identical protein binding activity. Predicted to be involved in adaptive immune response. Predicted to act upstream of or within regulation of natural killer cell activation. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303180 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021181.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF7	NM_021181.5	MANE Select	c.937-346A>C		intron	N/A	NP_067004.3
	SLAMF7	NM_001282592.2		c.833-346A>C		intron	N/A	NP_001269521.1
	SLAMF7	NM_001282594.2		c.655-346A>C		intron	N/A	NP_001269523.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF7	ENST00000368043.8	TSL:1 MANE Select	c.937-346A>C		intron	N/A	ENSP00000357022.3
	SLAMF7	ENST00000359331.8	TSL:1	c.833-346A>C		intron	N/A	ENSP00000352281.4
	SLAMF7	ENST00000368042.7	TSL:1	c.616-346A>C		intron	N/A	ENSP00000357021.3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
DANN	Benign	0.45
PhyloP100		-0.56

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: rs489286; hg19: chr1-160722550;