chrX-71229952-A-G

Variant names:

• chrX-71229952-A-G
• rs752081

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 0.377 in 110,222 control chromosomes in the GnomAD database, including 6,409 homozygotes. There are 11,758 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 0.38 (6409 hom., 11758 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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: 0.377 AC: 41499 AN: 110166 Hom.: 6401 Cov.: 22

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.281

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.377 AC: 41530 AN: 110222 Hom.: 6409 Cov.: 22 AF XY: 0.362 AC XY: 11758 AN XY: 32502

African (AFR) AF: 0.563 AC: 16993 AN: 30192

American (AMR) AF: 0.466 AC: 4790 AN: 10281

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 676 AN: 2633

East Asian (EAS) AF: 0.245 AC: 853 AN: 3476

South Asian (SAS) AF: 0.222 AC: 581 AN: 2620

European-Finnish (FIN) AF: 0.304 AC: 1771 AN: 5824

Middle Eastern (MID) AF: 0.285 AC: 61 AN: 214

European-Non Finnish (NFE) AF: 0.285 AC: 15047 AN: 52807

Other (OTH) AF: 0.358 AC: 538 AN: 1501

Alfa AF: 0.325 Hom.: 27102

Bravo AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752081; hg19: chrX-70449802;