1-160750417-C-T

Variant names:

• chr1-160750417-C-T
• rs768547449
• NM_021181.5:c.763C>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_021181.5(SLAMF7):​c.763C>T​(p.Gln255*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLAMF7 NM_021181.5 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.763C>T	p.Gln255*	stop_gained	Exon 4 of 7	NP_067004.3
	SLAMF7	NM_001282592.2		c.763C>T	p.Gln255*	stop_gained	Exon 4 of 6	NP_001269521.1	Q9NQ25-5
	SLAMF7	NM_001282594.2		c.481C>T	p.Gln161*	stop_gained	Exon 3 of 6	NP_001269523.1	B4DW98

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF7	ENST00000368043.8	TSL:1 MANE Select	c.763C>T	p.Gln255*	stop_gained	Exon 4 of 7	ENSP00000357022.3	Q9NQ25-1
	SLAMF7	ENST00000359331.8	TSL:1	c.763C>T	p.Gln255*	stop_gained	Exon 4 of 6	ENSP00000352281.4	Q9NQ25-5
	SLAMF7	ENST00000368042.7	TSL:1	c.442C>T	p.Gln148*	stop_gained	Exon 3 of 6	ENSP00000357021.3	Q9NQ25-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Uncertain	25
DANN	Benign	0.94
Eigen	Benign	-0.49
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.059	N
PhyloP100		-1.2
Vest4		0.47
GERP RS		-5.9
Mutation Taster		=99/101	disease causing (fs/PTC)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.18		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: rs768547449; hg19: chr1-160720207;