chrX-85634049-C-A

Position:

• chrX-85634049-C-A

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 0.552 in 108,977 control chromosomes in the GnomAD database, including 13,463 homozygotes. There are 16,685 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 0.55 (13463 hom., 16685 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.552 AC: 60132 AN: 108947 Hom.: 13468 Cov.: 21 AF XY: 0.532 AC XY: 16647 AN XY: 31299

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.565

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.552 AC: 60157 AN: 108977 Hom.: 13463 Cov.: 21 AF XY: 0.532 AC XY: 16685 AN XY: 31339

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.526

Alfa AF: 0.496 Hom.: 11841

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7882767; hg19: chrX-84889054;