X-15219931-T-C

Variant names:

• chrX-15219931-T-C
• rs2054513

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 0.424 in 109,807 control chromosomes in the GnomAD database, including 7,881 homozygotes. There are 13,623 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 0.42 (7881 hom., 13623 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.424 AC: 46552 AN: 109756 Hom.: 7877 Cov.: 22

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.424 AC: 46569 AN: 109807 Hom.: 7881 Cov.: 22 AF XY: 0.424 AC XY: 13623 AN XY: 32113

African (AFR) AF: 0.206 AC: 6264 AN: 30381

American (AMR) AF: 0.533 AC: 5468 AN: 10255

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 1631 AN: 2607

East Asian (EAS) AF: 0.686 AC: 2348 AN: 3422

South Asian (SAS) AF: 0.458 AC: 1167 AN: 2547

European-Finnish (FIN) AF: 0.480 AC: 2743 AN: 5712

Middle Eastern (MID) AF: 0.457 AC: 95 AN: 208

European-Non Finnish (NFE) AF: 0.495 AC: 26015 AN: 52518

Other (OTH) AF: 0.465 AC: 691 AN: 1487

Alfa AF: 0.420 Hom.: 4148

Bravo AF: 0.425

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.71
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2054513; hg19: chrX-15238053;