1-160752760-A-G

Variant names:

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

Variant summary

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

The NM_021181.5(SLAMF7):​c.937-346A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,952 control chromosomes in the GnomAD database, including 32,676 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 0.65 (32676 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

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>G		intron	N/A	NP_067004.3
	SLAMF7	NM_001282592.2		c.833-346A>G		intron	N/A	NP_001269521.1
	SLAMF7	NM_001282594.2		c.655-346A>G		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>G		intron	N/A	ENSP00000357022.3
	SLAMF7	ENST00000359331.8	TSL:1	c.833-346A>G		intron	N/A	ENSP00000352281.4
	SLAMF7	ENST00000368042.7	TSL:1	c.616-346A>G		intron	N/A	ENSP00000357021.3

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98597 AN: 151834 Hom.: 32662 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.649 AC: 98642 AN: 151952 Hom.: 32676 Cov.: 31 AF XY: 0.655 AC XY: 48632 AN XY: 74278

African (AFR) AF: 0.518 AC: 21455 AN: 41400

American (AMR) AF: 0.765 AC: 11687 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2502 AN: 3462

East Asian (EAS) AF: 0.803 AC: 4153 AN: 5172

South Asian (SAS) AF: 0.747 AC: 3607 AN: 4826

European-Finnish (FIN) AF: 0.703 AC: 7416 AN: 10546

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45566 AN: 67946

Other (OTH) AF: 0.683 AC: 1441 AN: 2110

Alfa AF: 0.666 Hom.: 133926

Bravo AF: 0.648

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.35
DANN	Benign	0.47
PhyloP100		-0.56
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: rs489286; hg19: chr1-160722550;