rs5002947

Positions:

• chr1-160608351-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.*2397G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,044 control chromosomes in the GnomAD database, including 7,816 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 0.31 (7816 hom., cov: 31)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: SLAMF1 NM_003037.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAMF1	NM_003037.5	c.*2397G>A		3_prime_UTR_variant	7/7	ENST00000302035.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF1	ENST00000302035.11	c.*2397G>A		3_prime_UTR_variant	7/7	1	NM_003037.5	P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47725 AN: 151910 Hom.: 7814 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.100

GnomAD4 genome AF: 0.314 AC: 47736 AN: 152028 Hom.: 7816 Cov.: 31 AF XY: 0.307 AC XY: 22792 AN XY: 74306

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.342

Alfa AF: 0.333 Hom.: 8532

Bravo AF: 0.322

Asia WGS AF: 0.216 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.82

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: rs5002947; hg19: chr1-160578141;