rs5936441

Positions:

• chrX-148242736-C-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 0.451 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;