X-110531426-G-T

Variant names:

• chrX-110531426-G-T
• rs12849634

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 0.417 in 110,298 control chromosomes in the GnomAD database, including 7,685 homozygotes. There are 12,781 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 0.42 (7685 hom., 12781 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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: 0.417 AC: 45980 AN: 110246 Hom.: 7690 Cov.: 22

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.417 AC: 45987 AN: 110298 Hom.: 7685 Cov.: 22 AF XY: 0.392 AC XY: 12781 AN XY: 32634

African (AFR) AF: 0.559 AC: 16857 AN: 30157

American (AMR) AF: 0.287 AC: 2994 AN: 10440

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1199 AN: 2629

East Asian (EAS) AF: 0.0144 AC: 51 AN: 3540

South Asian (SAS) AF: 0.221 AC: 570 AN: 2583

European-Finnish (FIN) AF: 0.377 AC: 2210 AN: 5865

Middle Eastern (MID) AF: 0.344 AC: 74 AN: 215

European-Non Finnish (NFE) AF: 0.400 AC: 21070 AN: 52683

Other (OTH) AF: 0.384 AC: 580 AN: 1511

Alfa AF: 0.406 Hom.: 2360

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs12849634; hg19: chrX-109774654;