chrX-95025411-G-C

Variant names:

• chrX-95025411-G-C
• rs1166756

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.395 AC: 43380 AN: 109917 Hom.: 6933 Cov.: 22 AF XY: 0.395 AC XY: 12722 AN XY: 32225

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.448

Alfa AF: 0.188 Hom.: 792

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1166756; hg19: chrX-94280410;