rs763299

Positions:

• chrX-112871491-T-C

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 0.105 in 111,221 control chromosomes in the GnomAD database, including 1,138 homozygotes. There are 3,184 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 0.10 (1138 hom., 3184 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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: 0.104 AC: 11617 AN: 111173 Hom.: 1138 Cov.: 22 AF XY: 0.0946 AC XY: 3157 AN XY: 33385

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.00116

Gnomad MID AF: 0.0460

Gnomad NFE AF: 0.00427

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.105 AC: 11645 AN: 111221 Hom.: 1138 Cov.: 22 AF XY: 0.0952 AC XY: 3184 AN XY: 33443

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.00116

Gnomad4 NFE AF: 0.00427

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0595 Hom.: 299

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763299; hg19: chrX-112114719;