rs7063116

chrX-50492002-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 0.379 in 111,066 control chromosomes in the GnomAD database, including 6,492 homozygotes. There are 12,120 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 0.38 (6492 hom., 12120 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.379 AC: 42108 AN: 111019 Hom.: 6490 Cov.: 23 AF XY: 0.363 AC XY: 12089 AN XY: 33271

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.379 AC: 42139 AN: 111066 Hom.: 6492 Cov.: 23 AF XY: 0.364 AC XY: 12120 AN XY: 33328

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.372

Alfa AF: 0.347 Hom.: 4107

Bravo AF: 0.406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7063116; hg19: chrX-50235002;