X-95025411-G-C

Position:

• chrX-95025411-G-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.95025411G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;