rs5935419

Variant names:

• chrX-12847809-C-T
• rs5935419

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;