rs2413808

Variant names:

• chr15-46417110-G-A
• rs2413808
• ENST00000661853.1:n.45+6757G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-46417110-G-A
• chr15-46417110-G-C

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.45+6757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,146 control chromosomes in the GnomAD database, including 70,483 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 0.96 (70483 hom., cov: 30)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 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
ENSG00000287704	ENST00000661853.1	n.45+6757G>A		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.56+6757G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146192 AN: 152028 Hom.: 70433 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.962 AC: 146301 AN: 152146 Hom.: 70483 Cov.: 30 AF XY: 0.962 AC XY: 71571 AN XY: 74394

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.985

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.974

Alfa AF: 0.986 Hom.: 86401

Bravo AF: 0.959

Asia WGS AF: 0.988 AC: 3436 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	0.75
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413808; hg19: chr15-46709308;