X-95859612-C-T

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 0.385 in 109,010 control chromosomes in the GnomAD database, including 6,921 homozygotes. There are 11,942 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 (6921 hom., 11942 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.385 AC: 41948 AN: 108965 Hom.: 6920 Cov.: 22 AF XY: 0.377 AC XY: 11902 AN XY: 31531

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.385 AC: 41989 AN: 109010 Hom.: 6921 Cov.: 22 AF XY: 0.378 AC XY: 11942 AN XY: 31586

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.354

Alfa AF: 0.276 Hom.: 12988

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.13
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857602; hg19: chrX-95114611; COSMIC: COSV70048366;