rs10917825

Variant names:

• chr1-163730402-G-A
• rs10917825
• ENST00000725058.1:n.213-5112G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-163730402-G-A
• chr1-163730402-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725058.1(ENSG00000294659):​n.213-5112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,032 control chromosomes in the GnomAD database, including 13,437 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 0.41 (13437 hom., cov: 32)
• Consequence: ENSG00000294659 ENST00000725058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 3 publications found

Genes affected

ENSG00000294659 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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
ENSG00000294659	ENST00000725058.1	n.213-5112G>A		intron_variant	Intron 2 of 4
ENSG00000294659	ENST00000725059.1	n.213-5112G>A		intron_variant	Intron 2 of 5
ENSG00000294659	ENST00000725060.1	n.60-5112G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61941 AN: 151914 Hom.: 13425 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.408 AC: 61989 AN: 152032 Hom.: 13437 Cov.: 32 AF XY: 0.416 AC XY: 30899 AN XY: 74290

African (AFR) AF: 0.287 AC: 11922 AN: 41496

American (AMR) AF: 0.421 AC: 6433 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3728 AN: 5154

South Asian (SAS) AF: 0.558 AC: 2681 AN: 4804

European-Finnish (FIN) AF: 0.504 AC: 5308 AN: 10536

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29359 AN: 67984

Other (OTH) AF: 0.398 AC: 840 AN: 2110

Alfa AF: 0.407 Hom.: 5358

Bravo AF: 0.397

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10917825; hg19: chr1-163699639;