chrX-80918441-C-T

Variant names:

• chrX-80918441-C-T
• rs7056400

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;