rs5935419

Positions:

• chrX-12847809-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 0.0962 in 110,182 control chromosomes in the GnomAD database, including 568 homozygotes. There are 2,885 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 0.096 (568 hom., 2885 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.0961 AC: 10581 AN: 110128 Hom.: 569 Cov.: 22 AF XY: 0.0884 AC XY: 2866 AN XY: 32416

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0469

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0388

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0962 AC: 10601 AN: 110182 Hom.: 568 Cov.: 22 AF XY: 0.0888 AC XY: 2885 AN XY: 32480

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0388

Gnomad4 EAS AF: 0.0317

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0471

Gnomad4 NFE AF: 0.0534

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0654 Hom.: 3080

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5935419; hg19: chrX-12865928;