2-75957690-C-T

Variant names:

• chr2-75957690-C-T
• rs2583526
• ENST00000670606.1:n.764+85198C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670606.1(ENSG00000287474):​n.764+85198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,868 control chromosomes in the GnomAD database, including 29,626 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 0.62 (29626 hom., cov: 31)
• Consequence: ENSG00000287474 ENST00000670606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287474	ENST00000670606.1	n.764+85198C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93830 AN: 151756 Hom.: 29570 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.619 AC: 93950 AN: 151868 Hom.: 29626 Cov.: 31 AF XY: 0.624 AC XY: 46265 AN XY: 74196

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.581

Alfa AF: 0.552 Hom.: 39392

Bravo AF: 0.628

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2583526; hg19: chr2-76184816;