rs5916245

Variant names:

• chrX-5743495-T-C
• rs5916245

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;