rs5913060

Variant names:

• chrX-79727276-G-A
• rs5913060

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;