1-160610225-A-G

Variant names:

• chr1-160610225-A-G
• rs1061217
• NM_003037.5:c.*523T>C

Variant summary

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

The NM_003037.5(SLAMF1):​c.*523T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 447,572 control chromosomes in the GnomAD database, including 68,560 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 0.48 (20046 hom., cov: 32)
  • Exomes 𝑓: 0.56 (48514 hom.)
• Consequence: SLAMF1 NM_003037.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 19 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.*523T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.*523T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_003037.5	ENSP00000306190.6

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73701 AN: 151974 Hom.: 20035 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.565 AC: 166883 AN: 295480 Hom.: 48514 Cov.: 0 AF XY: 0.564 AC XY: 94914 AN XY: 168420

African (AFR) AF: 0.223 AC: 1806 AN: 8104

American (AMR) AF: 0.461 AC: 11595 AN: 25170

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 5929 AN: 10422

East Asian (EAS) AF: 0.683 AC: 6191 AN: 9070

South Asian (SAS) AF: 0.539 AC: 31233 AN: 57930

European-Finnish (FIN) AF: 0.695 AC: 8803 AN: 12658

Middle Eastern (MID) AF: 0.406 AC: 1111 AN: 2734

European-Non Finnish (NFE) AF: 0.596 AC: 92659 AN: 155568

Other (OTH) AF: 0.547 AC: 7556 AN: 13824

GnomAD4 genome AF: 0.485 AC: 73735 AN: 152092 Hom.: 20046 Cov.: 32 AF XY: 0.490 AC XY: 36429 AN XY: 74340

African (AFR) AF: 0.229 AC: 9503 AN: 41498

American (AMR) AF: 0.459 AC: 7007 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3528 AN: 5182

South Asian (SAS) AF: 0.550 AC: 2648 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7203 AN: 10566

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40180 AN: 67964

Other (OTH) AF: 0.471 AC: 994 AN: 2112

Alfa AF: 0.547 Hom.: 71436

Bravo AF: 0.458

Asia WGS AF: 0.557 AC: 1935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.015
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: rs1061217; hg19: chr1-160580015; COSMIC: COSV52497717; COSMIC: COSV52497717;