X-891996-G-T

Position:

• chrX-891996-G-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 0.122 in 152,032 control chromosomes in the GnomAD database, including 2,997 homozygotes. There are 8,960 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 0.12 (2997 hom., 8960 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18523 AN: 151914 Hom.: 2978 Cov.: 32 AF XY: 0.120 AC XY: 8907 AN XY: 74196

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.00331

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.122 AC: 18584 AN: 152032 Hom.: 2997 Cov.: 32 AF XY: 0.121 AC XY: 8960 AN XY: 74324

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.0325

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0971

Bravo AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4497142; hg19: chrX-852731;