rs2753260

chr1-160618805-C-Achr1-160618805-C-Gchr1-160618805-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.864+971G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,060 control chromosomes in the GnomAD database, including 45,502 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 0.77 (45502 hom., cov: 31)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAMF1	NM_003037.5	c.864+971G>T		intron_variant		ENST00000302035.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAMF1	ENST00000302035.11	c.864+971G>T		intron_variant		1	NM_003037.5	P1
SLAMF1	ENST00000538290.2	c.947+971G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116877 AN: 151942 Hom.: 45451 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.769 AC: 116989 AN: 152060 Hom.: 45502 Cov.: 31 AF XY: 0.777 AC XY: 57781 AN XY: 74330

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.736

Alfa AF: 0.708 Hom.: 50264

Bravo AF: 0.769

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.72

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: rs2753260; hg19: chr1-160588595;