rs962458

Variant names:

• chrX-67526122-A-G
• rs962458

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.216 AC: 23990 AN: 110940 Hom.: 4231 Cov.: 22

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

African (AFR) AF: 0.602 AC: 18179 AN: 30210

American (AMR) AF: 0.0863 AC: 904 AN: 10475

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 73 AN: 2649

East Asian (EAS) AF: 0.00114 AC: 4 AN: 3521

South Asian (SAS) AF: 0.0569 AC: 151 AN: 2655

European-Finnish (FIN) AF: 0.0609 AC: 368 AN: 6041

Middle Eastern (MID) AF: 0.106 AC: 23 AN: 216

European-Non Finnish (NFE) AF: 0.0758 AC: 4019 AN: 53019

Other (OTH) AF: 0.157 AC: 239 AN: 1523

Alfa AF: 0.0974 Hom.: 3137

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
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs962458; hg19: chrX-66745964;