chr1-160645887-C-T

Variant names:

• chr1-160645887-C-T
• rs10489635
• NM_003037.5:c.76+983G>A

Variant summary

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

The NM_003037.5(SLAMF1):​c.76+983G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,108 control chromosomes in the GnomAD database, including 230 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 0.048 (230 hom., cov: 32)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.76+983G>A		intron_variant	Intron 1 of 6	ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.76+983G>A		intron_variant	Intron 1 of 6	1	NM_003037.5	ENSP00000306190.6
SLAMF1	ENST00000538290.2	c.76+983G>A		intron_variant	Intron 1 of 7	1		ENSP00000438406.2
SLAMF1	ENST00000494463.1	n.152+983G>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7306 AN: 151990 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0480 AC: 7308 AN: 152108 Hom.: 230 Cov.: 32 AF XY: 0.0467 AC XY: 3476 AN XY: 74360

African (AFR) AF: 0.0896 AC: 3715 AN: 41460

American (AMR) AF: 0.0317 AC: 485 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3466

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5176

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4822

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2204 AN: 67994

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0391 Hom.: 376

Bravo AF: 0.0492

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.90
PhyloP100		-0.20
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: rs10489635; hg19: chr1-160615677;