X-95210581-T-G

Variant names:

• chrX-95210581-T-G
• rs1372687

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 0.358 in 109,893 control chromosomes in the GnomAD database, including 5,405 homozygotes. There are 11,408 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 0.36 (5405 hom., 11408 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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: 0.357 AC: 39261 AN: 109862 Hom.: 5402 Cov.: 22

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.233

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.358 AC: 39294 AN: 109893 Hom.: 5405 Cov.: 22 AF XY: 0.353 AC XY: 11408 AN XY: 32323

African (AFR) AF: 0.457 AC: 13876 AN: 30394

American (AMR) AF: 0.434 AC: 4460 AN: 10279

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 696 AN: 2631

East Asian (EAS) AF: 0.562 AC: 1960 AN: 3486

South Asian (SAS) AF: 0.485 AC: 1289 AN: 2659

European-Finnish (FIN) AF: 0.251 AC: 1373 AN: 5463

Middle Eastern (MID) AF: 0.230 AC: 47 AN: 204

European-Non Finnish (NFE) AF: 0.285 AC: 14981 AN: 52599

Other (OTH) AF: 0.322 AC: 485 AN: 1508

Alfa AF: 0.314 Hom.: 25974

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.59
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs1372687; hg19: chrX-94465580;