X-850871-C-T

Variant names:

• chrX-850871-C-T
• rs5946325

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 0.761 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.761 AC: 115231 AN: 151446 Hom.: 44426 Cov.: 29 AF XY: 0.763 AC XY: 56413 AN XY: 73902

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

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.757

Bravo AF: 0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946325; hg19: chrX-811606;