rs5935419

Variant names:

• chrX-12847809-C-T
• rs5935419

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 10581 AN: 110128 Hom.: 569 Cov.: 22

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

African (AFR) AF: 0.207 AC: 6223 AN: 30059

American (AMR) AF: 0.0595 AC: 614 AN: 10324

Ashkenazi Jewish (ASJ) AF: 0.0388 AC: 102 AN: 2631

East Asian (EAS) AF: 0.0317 AC: 112 AN: 3537

South Asian (SAS) AF: 0.102 AC: 261 AN: 2558

European-Finnish (FIN) AF: 0.0471 AC: 275 AN: 5838

Middle Eastern (MID) AF: 0.101 AC: 22 AN: 218

European-Non Finnish (NFE) AF: 0.0534 AC: 2820 AN: 52841

Other (OTH) AF: 0.0938 AC: 140 AN: 1493

Alfa AF: 0.0725 Hom.: 4921

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.70
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs5935419; hg19: chrX-12865928;