X-67288544-A-T

Position:

• chrX-67288544-A-T

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 0.634 in 110,515 control chromosomes in the GnomAD database, including 19,218 homozygotes. There are 21,170 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 0.63 (19218 hom., 21170 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681

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 (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.634 AC: 70045 AN: 110465 Hom.: 19227 Cov.: 23 AF XY: 0.647 AC XY: 21160 AN XY: 32697

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.634 AC: 70031 AN: 110515 Hom.: 19218 Cov.: 23 AF XY: 0.646 AC XY: 21170 AN XY: 32757

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.682

Alfa AF: 0.708 Hom.: 5934

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521339; hg19: chrX-66508386;