rs10855652

Variant names:

• chrX-87161871-G-A
• rs10855652

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 0.461 in 109,308 control chromosomes in the GnomAD database, including 8,708 homozygotes. There are 14,022 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 0.46 (8708 hom., 14022 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.534 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: 0.461 AC: 50413 AN: 109261 Hom.: 8708 Cov.: 21 AF XY: 0.443 AC XY: 13996 AN XY: 31615

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.461 AC: 50438 AN: 109308 Hom.: 8708 Cov.: 21 AF XY: 0.443 AC XY: 14022 AN XY: 31672

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.461

Alfa AF: 0.475 Hom.: 35232

Bravo AF: 0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10855652; hg19: chrX-86416874;