rs5913060

Positions:

• chrX-79727276-G-A
• chrX-79727276-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 0.232 in 108,678 control chromosomes in the GnomAD database, including 2,350 homozygotes. There are 6,903 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 0.23 (2350 hom., 6903 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 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: 0.232 AC: 25245 AN: 108625 Hom.: 2347 Cov.: 21 AF XY: 0.222 AC XY: 6888 AN XY: 31045

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.232 AC: 25262 AN: 108678 Hom.: 2350 Cov.: 21 AF XY: 0.222 AC XY: 6903 AN XY: 31108

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.222

Alfa AF: 0.108 Hom.: 551

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5913060; hg19: chrX-78982773;