X-30269140-A-G

Position:

• chrX-30269140-A-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 0.399 in 109,800 control chromosomes in the GnomAD database, including 6,684 homozygotes. There are 12,265 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 0.40 (6684 hom., 12265 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.399 AC: 43775 AN: 109748 Hom.: 6685 Cov.: 22 AF XY: 0.381 AC XY: 12238 AN XY: 32086

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.399 AC: 43802 AN: 109800 Hom.: 6684 Cov.: 22 AF XY: 0.382 AC XY: 12265 AN XY: 32148

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.354

Alfa AF: 0.406 Hom.: 3250

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521956; hg19: chrX-30287257;