rs5946760

Variant names:

• chrX-745607-A-G
• rs5946760

Your query was ambiguous. Multiple possible variants found:

• chrX-745607-A-G
• chrX-745607-A-T

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 0.269 in 151,866 control chromosomes in the GnomAD database, including 5,979 homozygotes. There are 19,690 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 0.27 (5979 hom., 19690 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 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: 0.269 AC: 40817 AN: 151748 Hom.: 5966 Cov.: 31 AF XY: 0.265 AC XY: 19635 AN XY: 74104

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.269 AC: 40858 AN: 151866 Hom.: 5979 Cov.: 31 AF XY: 0.265 AC XY: 19690 AN XY: 74232

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.236

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946760; hg19: chrX-706342;