chrX-84676639-T-C

Variant names:

• chrX-84676639-T-C
• rs830249

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 0.184 in 110,570 control chromosomes in the GnomAD database, including 1,782 homozygotes. There are 5,586 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 0.18 (1782 hom., 5586 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.184 AC: 20292 AN: 110517 Hom.: 1783 Cov.: 22 AF XY: 0.169 AC XY: 5574 AN XY: 32965

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0936

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.184 AC: 20309 AN: 110570 Hom.: 1782 Cov.: 22 AF XY: 0.169 AC XY: 5586 AN XY: 33028

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.138

Alfa AF: 0.166 Hom.: 952

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.5
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs830249; hg19: chrX-83931647;