rs5916542

Variant names:

• chrX-4232853-A-T
• rs5916542

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 0.412 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.412 AC: 45750 AN: 111127 Hom.: 7047 Cov.: 23

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

African (AFR) AF: 0.448 AC: 13698 AN: 30568

American (AMR) AF: 0.313 AC: 3296 AN: 10518

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1163 AN: 2643

East Asian (EAS) AF: 0.0943 AC: 334 AN: 3543

South Asian (SAS) AF: 0.225 AC: 596 AN: 2645

European-Finnish (FIN) AF: 0.399 AC: 2378 AN: 5955

Middle Eastern (MID) AF: 0.415 AC: 88 AN: 212

European-Non Finnish (NFE) AF: 0.440 AC: 23275 AN: 52907

Other (OTH) AF: 0.401 AC: 609 AN: 1519

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs5916542; hg19: chrX-4150894;