chr1-160620975-C-T

Position:

• chr1-160620975-C-T

Variant summary

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

The NM_003037.5(SLAMF1):​c.791-1126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,080 control chromosomes in the GnomAD database, including 21,880 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 0.51 (21880 hom., cov: 33)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

Genes affected

SLAMF1 (HGNC:10903): (signaling lymphocytic activation molecule family member 1) Enables SH2 domain binding activity and identical protein binding activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.791-1126G>A		intron_variant		ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.791-1126G>A		intron_variant		1	NM_003037.5	ENSP00000306190	P1
SLAMF1	ENST00000538290.2	c.874-1126G>A		intron_variant		1		ENSP00000438406

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77866 AN: 151962 Hom.: 21858 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.512 AC: 77919 AN: 152080 Hom.: 21880 Cov.: 33 AF XY: 0.527 AC XY: 39178 AN XY: 74330

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.526

Alfa AF: 0.543 Hom.: 22835

Bravo AF: 0.499

Asia WGS AF: 0.762 AC: 2646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs164283; hg19: chr1-160590765;