X-8945785-T-C

Variant names:

• chrX-8945785-T-C
• rs5934505

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 0.274 in 111,324 control chromosomes in the GnomAD database, including 3,172 homozygotes. There are 8,794 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 (3172 hom., 8794 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.274 AC: 30450 AN: 111276 Hom.: 3172 Cov.: 23 AF XY: 0.262 AC XY: 8778 AN XY: 33502

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.374

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.274 AC: 30466 AN: 111324 Hom.: 3172 Cov.: 23 AF XY: 0.262 AC XY: 8794 AN XY: 33560

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.286

Alfa AF: 0.273 Hom.: 22356

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5934505; hg19: chrX-8913826;