rs5916544

Variant names:

• chrX-4233009-G-A
• rs5916544

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 110,164 control chromosomes in the GnomAD database, including 7,053 homozygotes. There are 12,793 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 (7053 hom., 12793 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.412 AC: 45413 AN: 110111 Hom.: 7051 Cov.: 23 AF XY: 0.394 AC XY: 12764 AN XY: 32403

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.412 AC: 45428 AN: 110164 Hom.: 7053 Cov.: 23 AF XY: 0.394 AC XY: 12793 AN XY: 32466

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.396

Alfa AF: 0.385 Hom.: 7844

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5916544; hg19: chrX-4151050;