rs10465428

chrX-117565503-C-AchrX-117565503-C-GchrX-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;