chr1-160622207-T-C

Variant names:

• chr1-160622207-T-C
• rs16832283
• NM_003037.5:c.790+1889A>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.790+1889A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,912 control chromosomes in the GnomAD database, including 9,011 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 0.32 (9011 hom., cov: 31)
• Consequence: SLAMF1 NM_003037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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.790+1889A>G		intron	N/A	NP_003028.1	Q13291-1
	SLAMF1	NM_001330754.2		c.873+1296A>G		intron	N/A	NP_001317683.1	Q13291-4
	SLAMF1	NR_104399.3		n.889+1889A>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.790+1889A>G		intron	N/A	ENSP00000306190.6	Q13291-1
	SLAMF1	ENST00000538290.2	TSL:1	c.873+1296A>G		intron	N/A	ENSP00000438406.2	Q13291-4
	SLAMF1	ENST00000878659.1		c.701-2358A>G		intron	N/A	ENSP00000548717.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49180 AN: 151796 Hom.: 8992 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.324 AC: 49236 AN: 151912 Hom.: 9011 Cov.: 31 AF XY: 0.314 AC XY: 23340 AN XY: 74284

African (AFR) AF: 0.487 AC: 20175 AN: 41404

American (AMR) AF: 0.248 AC: 3785 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3466

East Asian (EAS) AF: 0.123 AC: 637 AN: 5164

South Asian (SAS) AF: 0.153 AC: 735 AN: 4812

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10578

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19683 AN: 67902

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.301 Hom.: 29062

Bravo AF: 0.336

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		1.1
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: rs16832283; hg19: chr1-160591997;