rs5946519

Variant names:

• chrX-866662-G-C
• rs5946519

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 152,062 control chromosomes in the GnomAD database, including 1,239 homozygotes. There are 8,796 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 0.12 (1239 hom., 8796 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 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: 0.121 AC: 18460 AN: 151944 Hom.: 1236 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.122 AC: 18480 AN: 152062 Hom.: 1239 Cov.: 31 AF XY: 0.118 AC XY: 8796 AN XY: 74338

African (AFR) AF: 0.115 AC: 4781 AN: 41500

American (AMR) AF: 0.153 AC: 2332 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 297 AN: 3472

East Asian (EAS) AF: 0.0250 AC: 129 AN: 5170

South Asian (SAS) AF: 0.0806 AC: 389 AN: 4824

European-Finnish (FIN) AF: 0.0957 AC: 1012 AN: 10576

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9095 AN: 67964

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.30
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs5946519; hg19: chrX-827397;