rs5916245

Positions:

• chrX-5743495-T-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 0.302 in 111,042 control chromosomes in the GnomAD database, including 3,835 homozygotes. There are 9,833 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 0.30 (3835 hom., 9833 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.302 AC: 33542 AN: 110991 Hom.: 3839 Cov.: 23 AF XY: 0.296 AC XY: 9834 AN XY: 33223

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.302 AC: 33526 AN: 111042 Hom.: 3835 Cov.: 23 AF XY: 0.295 AC XY: 9833 AN XY: 33284

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.289

Alfa AF: 0.332 Hom.: 27343

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5916245; hg19: chrX-5661536;