X-151677903-T-G

Position:

• chrX-151677903-T-G

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 0.209 in 111,913 control chromosomes in the GnomAD database, including 1,918 homozygotes. There are 6,914 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 0.21 (1918 hom., 6914 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.294 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: 0.209 AC: 23356 AN: 111861 Hom.: 1916 Cov.: 24 AF XY: 0.203 AC XY: 6904 AN XY: 34067

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.209 AC: 23364 AN: 111913 Hom.: 1918 Cov.: 24 AF XY: 0.203 AC XY: 6914 AN XY: 34129

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.247

Alfa AF: 0.177 Hom.: 1444

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7878232; hg19: chrX-150846375;