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. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661853.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287704	ENST00000661853.1		n.45+6757G>A		intron	N/A
	ENSG00000287704	ENST00000686120.1		n.56+6757G>A		intron	N/A
	ENSG00000287704	ENST00000736459.1		n.46+6757G>A		intron	N/A

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

African (AFR) AF: 0.893 AC: 37044 AN: 41468

American (AMR) AF: 0.985 AC: 15063 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3469 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 0.989 AC: 4764 AN: 4816

European-Finnish (FIN) AF: 0.974 AC: 10323 AN: 10596

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67218 AN: 68026

Other (OTH) AF: 0.974 AC: 2061 AN: 2116

Alfa AF: 0.983 Hom.: 111678

Bravo AF: 0.959

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.24
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2413808;

hg19: chr15-46709308;