chr1-160752241-C-T

Variant names:

• chr1-160752241-C-T
• rs201344120
• NM_021181.5:c.929C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_021181.5(SLAMF7):​c.929C>T​(p.Pro310Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,611,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 28)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: SLAMF7 NM_021181.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.263
• Publications: 2 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.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08126062).

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.929C>T	p.Pro310Leu	missense	Exon 6 of 7	NP_067004.3
	SLAMF7	NM_001282594.2		c.647C>T	p.Pro216Leu	missense	Exon 5 of 6	NP_001269523.1	B4DW98
	SLAMF7	NM_001282590.2		c.608C>T	p.Pro203Leu	missense	Exon 5 of 6	NP_001269519.1	Q9NQ25-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF7	ENST00000368043.8	TSL:1 MANE Select	c.929C>T	p.Pro310Leu	missense	Exon 6 of 7	ENSP00000357022.3	Q9NQ25-1
	SLAMF7	ENST00000368042.7	TSL:1	c.608C>T	p.Pro203Leu	missense	Exon 5 of 6	ENSP00000357021.3	Q9NQ25-2
	SLAMF7	ENST00000359331.8	TSL:1	c.825C>T	p.Thr275Thr	synonymous	Exon 5 of 6	ENSP00000352281.4	Q9NQ25-5

Frequencies

GnomAD3 genomes AF: 0.0000724 AC: 11 AN: 151990 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000360 AC: 9 AN: 250234 AF XY: 0.0000370

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000545

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000442

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000212 AC: 31 AN: 1459552 Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 14 AN XY: 726214

African (AFR) AF: 0.000120 AC: 4 AN: 33404

American (AMR) AF: 0.00 AC: 0 AN: 44636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26074

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39626

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86088

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5748

European-Non Finnish (NFE) AF: 0.0000189 AC: 21 AN: 1110320

Other (OTH) AF: 0.0000332 AC: 2 AN: 60282

GnomAD4 genome AF: 0.0000723 AC: 11 AN: 152108 Hom.: 0 Cov.: 28 AF XY: 0.0000672 AC XY: 5 AN XY: 74368

African (AFR) AF: 0.000217 AC: 9 AN: 41496

American (AMR) AF: 0.00 AC: 0 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68004

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.0000574 Hom.: 0

Bravo AF: 0.0000378

ExAC AF: 0.0000412 AC: 5

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.45	T
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.56
FATHMM_MKL	Benign	0.085	N
LIST_S2	Benign	0.75	T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.081	T
MetaSVM	Benign	-1.1	T
PhyloP100		0.26
PrimateAI	Benign	0.35	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.028
Sift	Uncertain	0.011	D
Sift4G	Uncertain	0.0060	D
Polyphen		1.0	D
Vest4		0.31
MVP		0.67
MPC		0.25
ClinPred		0.39	T
GERP RS		0.41
Varity_R		0.098
gMVP		0.42
Mutation Taster		=98/2	polymorphism

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: rs201344120; hg19: chr1-160722031; COSMIC: COSV63562765; COSMIC: COSV63562765;