chrX-112871491-T-C

Variant names:

• chrX-112871491-T-C
• rs763299

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;