chrX-745607-A-G

Variant names:

• chrX-745607-A-G
• rs5946760

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 0.269 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40817 AN: 151748 Hom.: 5966 Cov.: 31

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

African (AFR) AF: 0.380 AC: 15742 AN: 41378

American (AMR) AF: 0.184 AC: 2813 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3472

East Asian (EAS) AF: 0.192 AC: 992 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2531 AN: 10546

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16370 AN: 67914

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.22
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs5946760; hg19: chrX-706342;