chrX-150935362-G-A

Position:

• chrX-150935362-G-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 0.243 in 111,036 control chromosomes in the GnomAD database, including 2,537 homozygotes. There are 7,974 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 0.24 (2537 hom., 7974 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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: 0.243 AC: 26926 AN: 110982 Hom.: 2531 Cov.: 23 AF XY: 0.240 AC XY: 7965 AN XY: 33182

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.230

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.243 AC: 26950 AN: 111036 Hom.: 2537 Cov.: 23 AF XY: 0.240 AC XY: 7974 AN XY: 33246

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.277

Alfa AF: 0.216 Hom.: 15020

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2128990; hg19: chrX-150103835;