chr1-160622207-T-C

Position:

• chr1-160622207-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

SLAMF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLAMF1	NM_003037.5	c.790+1889A>G		intron_variant		ENST00000302035.11	NP_003028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11	c.790+1889A>G		intron_variant		1	NM_003037.5	ENSP00000306190.6
SLAMF1	ENST00000538290.2	c.873+1296A>G		intron_variant		1		ENSP00000438406.2

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.324

Alfa AF: 0.296 Hom.: 11809

Bravo AF: 0.336

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832283; hg19: chr1-160591997;