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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.423 AC: 45849 AN: 108506 Hom.: 7693 Cov.: 21 AF XY: 0.437 AC XY: 13512 AN XY: 30924

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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.458

Alfa AF: 0.249 Hom.: 1171

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10465428; hg19: chrX-116699466;