rs10493982

Variant names:

• chr1-102706427-G-A
• rs10493982

Your query was ambiguous. Multiple possible variants found:

• chr1-102706427-G-A
• chr1-102706427-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 0.162 in 152,052 control chromosomes in the GnomAD database, including 2,085 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 0.16 (2085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.188 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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24688 AN: 151934 Hom.: 2086 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.162 AC: 24697 AN: 152052 Hom.: 2085 Cov.: 32 AF XY: 0.159 AC XY: 11845 AN XY: 74332

African (AFR) AF: 0.191 AC: 7932 AN: 41502

American (AMR) AF: 0.129 AC: 1968 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 903 AN: 3466

East Asian (EAS) AF: 0.0745 AC: 385 AN: 5168

South Asian (SAS) AF: 0.149 AC: 721 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1293 AN: 10578

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10876 AN: 67934

Other (OTH) AF: 0.166 AC: 349 AN: 2106

Alfa AF: 0.163 Hom.: 8109

Bravo AF: 0.163

Asia WGS AF: 0.0990 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.48
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10493982; hg19: chr1-103171983;