X-67288544-A-T

Variant names:

• chrX-67288544-A-T
• rs10521339

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 0.634 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 70045 AN: 110465 Hom.: 19227 Cov.: 23

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

African (AFR) AF: 0.133 AC: 4071 AN: 30600

American (AMR) AF: 0.817 AC: 8437 AN: 10327

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 2357 AN: 2633

East Asian (EAS) AF: 0.999 AC: 3472 AN: 3477

South Asian (SAS) AF: 0.916 AC: 2375 AN: 2593

European-Finnish (FIN) AF: 0.809 AC: 4658 AN: 5755

Middle Eastern (MID) AF: 0.755 AC: 157 AN: 208

European-Non Finnish (NFE) AF: 0.813 AC: 42896 AN: 52757

Other (OTH) AF: 0.682 AC: 1019 AN: 1494

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
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10521339; hg19: chrX-66508386;