rs5916542

chrX-4232853-A-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 0.412 in 111,181 control chromosomes in the GnomAD database, including 7,049 homozygotes. There are 13,128 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 0.41 (7049 hom., 13128 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.412 AC: 45750 AN: 111127 Hom.: 7047 Cov.: 23 AF XY: 0.393 AC XY: 13098 AN XY: 33339

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.412 AC: 45766 AN: 111181 Hom.: 7049 Cov.: 23 AF XY: 0.393 AC XY: 13128 AN XY: 33403

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.401

Alfa AF: 0.429 Hom.: 2930

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.98
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5916542; hg19: chrX-4150894;