rs962458

Positions:

• chrX-67526122-A-G

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 0.216 in 110,994 control chromosomes in the GnomAD database, including 4,231 homozygotes. There are 6,511 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 0.22 (4231 hom., 6511 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 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: 0.216 AC: 23990 AN: 110940 Hom.: 4231 Cov.: 22 AF XY: 0.195 AC XY: 6477 AN XY: 33218

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.216 AC: 24029 AN: 110994 Hom.: 4231 Cov.: 22 AF XY: 0.196 AC XY: 6511 AN XY: 33282

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.00114

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.157

Alfa AF: 0.103 Hom.: 2359

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962458; hg19: chrX-66745964;