rs5935438

chrX-12894903-G-C

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 0.403 in 110,417 control chromosomes in the GnomAD database, including 6,686 homozygotes. There are 12,697 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 0.40 (6686 hom., 12697 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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: 0.403 AC: 44515 AN: 110364 Hom.: 6682 Cov.: 22 AF XY: 0.388 AC XY: 12671 AN XY: 32628

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.403 AC: 44542 AN: 110417 Hom.: 6686 Cov.: 22 AF XY: 0.388 AC XY: 12697 AN XY: 32691

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.368

Alfa AF: 0.421 Hom.: 2863

Bravo AF: 0.398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.4
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5935438; hg19: chrX-12913022;