rs2862413

Variant names:

• chr3-176294777-G-A
• rs2862413
• ENST00000687649.1:n.414-4884C>T

Variant summary

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

The ENST00000687649.1(ENSG00000288895):​n.414-4884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 148,366 control chromosomes in the GnomAD database, including 16,448 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 0.47 (16448 hom., cov: 29)
• Consequence: ENSG00000288895 ENST00000687649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

ENSG00000288895 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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
ENSG00000288895	ENST00000687649.1	n.414-4884C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.470 AC: 69680 AN: 148248 Hom.: 16440 Cov.: 29

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.470 AC: 69733 AN: 148366 Hom.: 16448 Cov.: 29 AF XY: 0.474 AC XY: 34247 AN XY: 72266

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.472

Alfa AF: 0.471 Hom.: 7970

Bravo AF: 0.454

Asia WGS AF: 0.369 AC: 1282 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2862413; hg19: chr3-176012565;