1-160635073-A-T

Variant names:

• chr1-160635073-A-T
• rs3766362
• NM_003037.5:c.416-176T>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.416-176T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,058 control chromosomes in the GnomAD database, including 32,073 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 0.65 (32073 hom., cov: 31)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.416-176T>A		intron_variant	Intron 2 of 6	ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.416-176T>A		intron_variant	Intron 2 of 6	1	NM_003037.5	ENSP00000306190.6
SLAMF1	ENST00000538290.2	c.416-176T>A		intron_variant	Intron 2 of 7	1		ENSP00000438406.2

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98275 AN: 151940 Hom.: 32029 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.647 AC: 98377 AN: 152058 Hom.: 32073 Cov.: 31 AF XY: 0.650 AC XY: 48317 AN XY: 74338

African (AFR) AF: 0.650 AC: 26951 AN: 41452

American (AMR) AF: 0.629 AC: 9608 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2870 AN: 5162

South Asian (SAS) AF: 0.725 AC: 3495 AN: 4824

European-Finnish (FIN) AF: 0.690 AC: 7293 AN: 10564

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43834 AN: 67990

Other (OTH) AF: 0.632 AC: 1333 AN: 2108

Alfa AF: 0.651 Hom.: 4032

Bravo AF: 0.639

Asia WGS AF: 0.648 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.72
PhyloP100		0.26
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: rs3766362; hg19: chr1-160604863;