chrX-80918441-C-T

Position:

• chrX-80918441-C-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 0.114 in 110,390 control chromosomes in the GnomAD database, including 1,393 homozygotes. There are 3,524 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 0.11 (1393 hom., 3524 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.114 AC: 12578 AN: 110343 Hom.: 1394 Cov.: 22 AF XY: 0.107 AC XY: 3506 AN XY: 32669

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.00727

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0448

Gnomad EAS AF: 0.000284

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.0858

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0935

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

GnomAD4 genome AF: 0.114 AC: 12600 AN: 110390 Hom.: 1393 Cov.: 22 AF XY: 0.108 AC XY: 3524 AN XY: 32726

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0448

Gnomad4 EAS AF: 0.000284

Gnomad4 SAS AF: 0.0111

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0644 Hom.: 800

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7056400; hg19: chrX-80173940;