X-115003094-T-G

Variant names:

• chrX-115003094-T-G
• rs535036

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 0.273 in 110,944 control chromosomes in the GnomAD database, including 4,960 homozygotes. There are 8,285 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 0.27 (4960 hom., 8285 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.272 AC: 30186 AN: 110889 Hom.: 4954 Cov.: 22

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00480

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0965

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.273 AC: 30234 AN: 110944 Hom.: 4960 Cov.: 22 AF XY: 0.249 AC XY: 8285 AN XY: 33226

African (AFR) AF: 0.620 AC: 18772 AN: 30257

American (AMR) AF: 0.134 AC: 1408 AN: 10491

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 462 AN: 2647

East Asian (EAS) AF: 0.00482 AC: 17 AN: 3527

South Asian (SAS) AF: 0.117 AC: 311 AN: 2650

European-Finnish (FIN) AF: 0.0965 AC: 579 AN: 5997

Middle Eastern (MID) AF: 0.201 AC: 43 AN: 214

European-Non Finnish (NFE) AF: 0.155 AC: 8205 AN: 52974

Other (OTH) AF: 0.200 AC: 301 AN: 1508

Alfa AF: 0.199 Hom.: 2723

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.37
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs535036; hg19: chrX-114237657;