X-95025411-G-C

Variant names:

• chrX-95025411-G-C
• rs1166756

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 109,970 control chromosomes in the GnomAD database, including 6,927 homozygotes. There are 12,728 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 (6927 hom., 12728 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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: 0.395 AC: 43380 AN: 109917 Hom.: 6933 Cov.: 22

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.549

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.394 AC: 43366 AN: 109970 Hom.: 6927 Cov.: 22 AF XY: 0.394 AC XY: 12728 AN XY: 32288

African (AFR) AF: 0.159 AC: 4835 AN: 30411

American (AMR) AF: 0.560 AC: 5750 AN: 10261

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1040 AN: 2635

East Asian (EAS) AF: 0.464 AC: 1593 AN: 3433

South Asian (SAS) AF: 0.591 AC: 1515 AN: 2563

European-Finnish (FIN) AF: 0.415 AC: 2359 AN: 5684

Middle Eastern (MID) AF: 0.523 AC: 112 AN: 214

European-Non Finnish (NFE) AF: 0.476 AC: 25056 AN: 52606

Other (OTH) AF: 0.448 AC: 666 AN: 1487

Alfa AF: 0.188 Hom.: 792

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.60
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1166756; hg19: chrX-94280410;