1-160632458-C-T

Variant names:

• chr1-160632458-C-T
• rs6704124
• NM_003037.5:c.700+2155G>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.700+2155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,030 control chromosomes in the GnomAD database, including 7,282 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 0.30 (7282 hom., cov: 31)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.700+2155G>A		intron_variant	Intron 3 of 6	ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.700+2155G>A		intron_variant	Intron 3 of 6	1	NM_003037.5	ENSP00000306190.6
SLAMF1	ENST00000538290.2	c.700+2155G>A		intron_variant	Intron 3 of 7	1		ENSP00000438406.2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45747 AN: 151912 Hom.: 7288 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.301 AC: 45746 AN: 152030 Hom.: 7282 Cov.: 31 AF XY: 0.298 AC XY: 22121 AN XY: 74316

African (AFR) AF: 0.221 AC: 9185 AN: 41494

American (AMR) AF: 0.346 AC: 5289 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1862 AN: 5146

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4814

European-Finnish (FIN) AF: 0.277 AC: 2932 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23135 AN: 67930

Other (OTH) AF: 0.322 AC: 677 AN: 2102

Alfa AF: 0.328 Hom.: 35284

Bravo AF: 0.307

Asia WGS AF: 0.289 AC: 1010 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		0.0010
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: rs6704124; hg19: chr1-160602248;