rs10465428

Variant names:

• chrX-117565503-C-A
• rs10465428

Your query was ambiguous. Multiple possible variants found:

• chrX-117565503-C-A
• chrX-117565503-C-G
• chrX-117565503-C-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 0.422 in 108,561 control chromosomes in the GnomAD database, including 7,691 homozygotes. There are 13,536 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 0.42 (7691 hom., 13536 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.423 AC: 45849 AN: 108506 Hom.: 7693 Cov.: 21

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.422 AC: 45866 AN: 108561 Hom.: 7691 Cov.: 21 AF XY: 0.437 AC XY: 13536 AN XY: 30989

African (AFR) AF: 0.268 AC: 8013 AN: 29877

American (AMR) AF: 0.614 AC: 6162 AN: 10031

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1252 AN: 2615

East Asian (EAS) AF: 0.996 AC: 3367 AN: 3379

South Asian (SAS) AF: 0.759 AC: 1842 AN: 2426

European-Finnish (FIN) AF: 0.446 AC: 2489 AN: 5577

Middle Eastern (MID) AF: 0.481 AC: 103 AN: 214

European-Non Finnish (NFE) AF: 0.416 AC: 21777 AN: 52292

Other (OTH) AF: 0.458 AC: 675 AN: 1474

Alfa AF: 0.249 Hom.: 1171

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10465428; hg19: chrX-116699466;