chrX-850871-C-T

Variant names:

• chrX-850871-C-T
• rs5946325

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 0.761 in 151,564 control chromosomes in the GnomAD database, including 44,483 homozygotes. There are 56,533 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 0.76 (44483 hom., 56533 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.761 AC: 115231 AN: 151446 Hom.: 44426 Cov.: 29

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.761 AC: 115346 AN: 151564 Hom.: 44483 Cov.: 29 AF XY: 0.764 AC XY: 56533 AN XY: 74030

African (AFR) AF: 0.838 AC: 34668 AN: 41358

American (AMR) AF: 0.760 AC: 11552 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2090 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5108 AN: 5122

South Asian (SAS) AF: 0.852 AC: 4095 AN: 4804

European-Finnish (FIN) AF: 0.729 AC: 7663 AN: 10512

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47746 AN: 67808

Other (OTH) AF: 0.757 AC: 1586 AN: 2096

Bravo AF: 0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs5946325; hg19: chrX-811606;