rs1005295

Variant names:

• chrX-80086889-T-C
• rs1005295

Your query was ambiguous. Multiple possible variants found:

• chrX-80086889-T-C
• chrX-80086889-T-G

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 0.199 in 111,522 control chromosomes in the GnomAD database, including 1,598 homozygotes. There are 6,794 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 0.20 (1598 hom., 6794 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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: 0.199 AC: 22157 AN: 111473 Hom.: 1600 Cov.: 23

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.181

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.199 AC: 22152 AN: 111522 Hom.: 1598 Cov.: 23 AF XY: 0.201 AC XY: 6794 AN XY: 33724

African (AFR) AF: 0.149 AC: 4589 AN: 30800

American (AMR) AF: 0.131 AC: 1377 AN: 10499

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 399 AN: 2637

East Asian (EAS) AF: 0.227 AC: 805 AN: 3553

South Asian (SAS) AF: 0.388 AC: 1051 AN: 2706

European-Finnish (FIN) AF: 0.322 AC: 1897 AN: 5893

Middle Eastern (MID) AF: 0.189 AC: 41 AN: 217

European-Non Finnish (NFE) AF: 0.218 AC: 11543 AN: 53021

Other (OTH) AF: 0.183 AC: 280 AN: 1526

Alfa AF: 0.198 Hom.: 12699

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0010
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1005295; hg19: chrX-79342388;