chrX-102017519-G-T

Variant names:

• chrX-102017519-G-T
• rs2213392

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 0.394 in 110,791 control chromosomes in the GnomAD database, including 6,566 homozygotes. There are 12,438 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 0.39 (6566 hom., 12438 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.394 AC: 43601 AN: 110737 Hom.: 6565 Cov.: 23

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.394 AC: 43618 AN: 110791 Hom.: 6566 Cov.: 23 AF XY: 0.376 AC XY: 12438 AN XY: 33051

African (AFR) AF: 0.409 AC: 12459 AN: 30452

American (AMR) AF: 0.325 AC: 3386 AN: 10424

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1178 AN: 2635

East Asian (EAS) AF: 0.0121 AC: 43 AN: 3545

South Asian (SAS) AF: 0.220 AC: 582 AN: 2648

European-Finnish (FIN) AF: 0.321 AC: 1891 AN: 5896

Middle Eastern (MID) AF: 0.332 AC: 69 AN: 208

European-Non Finnish (NFE) AF: 0.435 AC: 22966 AN: 52793

Other (OTH) AF: 0.366 AC: 554 AN: 1515

Alfa AF: 0.416 Hom.: 43709

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.87
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2213392; hg19: chrX-101272492;