rs5002947

Variant names:

• chr1-160608351-C-T
• rs5002947
• NM_003037.5:c.*2397G>A

Variant summary

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

The NM_001330754.2(SLAMF1):​c.*2414G>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_001330754.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330754.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	NM_003037.5	MANE Select	c.*2397G>A		3_prime_UTR	Exon 7 of 7	NP_003028.1
	SLAMF1	NM_001330754.2		c.*2414G>A		3_prime_UTR	Exon 8 of 8	NP_001317683.1
	SLAMF1	NR_104399.3		n.3430G>A		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	ENST00000302035.11	TSL:1 MANE Select	c.*2397G>A		3_prime_UTR	Exon 7 of 7	ENSP00000306190.6
	SLAMF1	ENST00000878657.1		c.*2397G>A		3_prime_UTR	Exon 6 of 6	ENSP00000548716.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.344 AC: 14265 AN: 41476

American (AMR) AF: 0.289 AC: 4421 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3470

East Asian (EAS) AF: 0.175 AC: 902 AN: 5164

South Asian (SAS) AF: 0.202 AC: 971 AN: 4802

European-Finnish (FIN) AF: 0.240 AC: 2537 AN: 10572

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22335 AN: 67954

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.332 Hom.: 11019

Bravo AF: 0.322

Asia WGS AF: 0.216 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		-0.91
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: rs5002947; hg19: chr1-160578141;