rs1003682

Variant names:

• chrX-141903065-T-C
• rs1003682

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 0.245 in 110,171 control chromosomes in the GnomAD database, including 2,594 homozygotes. There are 7,749 hemizygotes in GnomAD. 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 0.25 (2594 hom., 7749 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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: 0.245 AC: 26987 AN: 110121 Hom.: 2593 Cov.: 22

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0490

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.245 AC: 27012 AN: 110171 Hom.: 2594 Cov.: 22 AF XY: 0.238 AC XY: 7749 AN XY: 32527

African (AFR) AF: 0.353 AC: 10612 AN: 30097

American (AMR) AF: 0.154 AC: 1620 AN: 10521

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 444 AN: 2630

East Asian (EAS) AF: 0.120 AC: 415 AN: 3467

South Asian (SAS) AF: 0.203 AC: 527 AN: 2590

European-Finnish (FIN) AF: 0.298 AC: 1747 AN: 5861

Middle Eastern (MID) AF: 0.209 AC: 45 AN: 215

European-Non Finnish (NFE) AF: 0.213 AC: 11210 AN: 52605

Other (OTH) AF: 0.238 AC: 359 AN: 1511

Alfa AF: 0.218 Hom.: 13237

Bravo AF: 0.241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.40
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1003682; hg19: chrX-140990851;