chr1-160616797-A-C

Variant names:

• chr1-160616797-A-C
• rs2089088
• NM_003037.5:c.864+2979T>G

Variant summary

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

The NM_003037.5(SLAMF1):​c.864+2979T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,134 control chromosomes in the GnomAD database, including 13,112 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 0.38 (13112 hom., cov: 32)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	NM_003037.5	MANE Select	c.864+2979T>G		intron	N/A	NP_003028.1	Q13291-1
	SLAMF1	NM_001330754.2		c.947+2979T>G		intron	N/A	NP_001317683.1	Q13291-4
	SLAMF1	NR_104399.3		n.890-4217T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	ENST00000302035.11	TSL:1 MANE Select	c.864+2979T>G		intron	N/A	ENSP00000306190.6	Q13291-1
	SLAMF1	ENST00000538290.2	TSL:1	c.947+2979T>G		intron	N/A	ENSP00000438406.2	Q13291-4
	SLAMF1	ENST00000878659.1		c.774+2979T>G		intron	N/A	ENSP00000548717.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58185 AN: 152016 Hom.: 13102 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.383 AC: 58228 AN: 152134 Hom.: 13112 Cov.: 32 AF XY: 0.392 AC XY: 29125 AN XY: 74368

African (AFR) AF: 0.138 AC: 5745 AN: 41546

American (AMR) AF: 0.379 AC: 5793 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3400 AN: 5182

South Asian (SAS) AF: 0.583 AC: 2817 AN: 4830

European-Finnish (FIN) AF: 0.534 AC: 5633 AN: 10550

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31785 AN: 67954

Other (OTH) AF: 0.376 AC: 795 AN: 2112

Alfa AF: 0.399 Hom.: 4438

Bravo AF: 0.358

Asia WGS AF: 0.546 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.64
PhyloP100		1.2
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: rs2089088; hg19: chr1-160586587;