rs10494580

Variant names:

• chr1-184383503-G-C
• rs10494580

Your query was ambiguous. Multiple possible variants found:

• chr1-184383503-G-C
• chr1-184383503-G-T

Variant summary

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

The variant allele was found at a frequency of 0.605 in 152,050 control chromosomes in the GnomAD database, including 31,133 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 0.61 (31133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91992 AN: 151932 Hom.: 31134 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.605 AC: 92016 AN: 152050 Hom.: 31133 Cov.: 32 AF XY: 0.610 AC XY: 45371 AN XY: 74324

African (AFR) AF: 0.268 AC: 11111 AN: 41444

American (AMR) AF: 0.725 AC: 11079 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3929 AN: 5172

South Asian (SAS) AF: 0.770 AC: 3706 AN: 4814

European-Finnish (FIN) AF: 0.693 AC: 7320 AN: 10558

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50059 AN: 67990

Other (OTH) AF: 0.672 AC: 1415 AN: 2106

Alfa AF: 0.564 Hom.: 2054

Bravo AF: 0.595

Asia WGS AF: 0.709 AC: 2460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10494580; hg19: chr1-184352637; COSMIC: COSV52410312;