rs10855652

Positions:

• chrX-87161871-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;