rs7063116

Variant names:

• chrX-50492002-G-A
• rs7063116

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.379 AC: 42108 AN: 111019 Hom.: 6490 Cov.: 23

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

African (AFR) AF: 0.580 AC: 17683 AN: 30481

American (AMR) AF: 0.404 AC: 4243 AN: 10502

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1031 AN: 2633

East Asian (EAS) AF: 0.136 AC: 486 AN: 3564

South Asian (SAS) AF: 0.152 AC: 406 AN: 2677

European-Finnish (FIN) AF: 0.254 AC: 1499 AN: 5908

Middle Eastern (MID) AF: 0.371 AC: 79 AN: 213

European-Non Finnish (NFE) AF: 0.300 AC: 15862 AN: 52906

Other (OTH) AF: 0.372 AC: 561 AN: 1509

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs7063116; hg19: chrX-50235002;