rs5936441

Variant names:

• chrX-148242736-C-T
• rs5936441

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 0.451 in 108,844 control chromosomes in the GnomAD database, including 9,588 homozygotes. There are 13,381 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 0.45 (9588 hom., 13381 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

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 = 0.728 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: 0.451 AC: 49065 AN: 108794 Hom.: 9585 Cov.: 21 AF XY: 0.428 AC XY: 13336 AN XY: 31188

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.451 AC: 49104 AN: 108844 Hom.: 9588 Cov.: 21 AF XY: 0.428 AC XY: 13381 AN XY: 31248

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.409

Alfa AF: 0.360 Hom.: 23312

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5936441; hg19: chrX-147324256;