rs10521667

Variant names:

• chrX-7897454-C-T
• rs10521667

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 0.0694 in 111,791 control chromosomes in the GnomAD database, including 649 homozygotes. There are 2,086 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 0.069 (649 hom., 2086 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 0 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 = 0.234 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 7752 AN: 111739 Hom.: 648 Cov.: 23

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.00641

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00183

Gnomad FIN AF: 0.000166

Gnomad MID AF: 0.0208

Gnomad NFE AF: 0.000770

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0694 AC: 7755 AN: 111791 Hom.: 649 Cov.: 23 AF XY: 0.0613 AC XY: 2086 AN XY: 34045

African (AFR) AF: 0.238 AC: 7300 AN: 30611

American (AMR) AF: 0.0293 AC: 310 AN: 10566

Ashkenazi Jewish (ASJ) AF: 0.00641 AC: 17 AN: 2652

East Asian (EAS) AF: 0.00 AC: 0 AN: 3579

South Asian (SAS) AF: 0.00183 AC: 5 AN: 2726

European-Finnish (FIN) AF: 0.000166 AC: 1 AN: 6019

Middle Eastern (MID) AF: 0.0230 AC: 5 AN: 217

European-Non Finnish (NFE) AF: 0.000770 AC: 41 AN: 53229

Other (OTH) AF: 0.0505 AC: 76 AN: 1505

Alfa AF: 0.0546 Hom.: 202

Bravo AF: 0.0807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.30
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10521667; hg19: chrX-7865495;