rs7054313

Variant names:

• chrX-83015810-G-A
• rs7054313

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 0.085 in 110,435 control chromosomes in the GnomAD database, including 294 homozygotes. There are 2,651 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 0.085 (294 hom., 2651 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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: 0.0850 AC: 9378 AN: 110382 Hom.: 293 Cov.: 22

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0844

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0850 AC: 9386 AN: 110435 Hom.: 294 Cov.: 22 AF XY: 0.0810 AC XY: 2651 AN XY: 32735

African (AFR) AF: 0.0872 AC: 2649 AN: 30363

American (AMR) AF: 0.0476 AC: 494 AN: 10381

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 272 AN: 2633

East Asian (EAS) AF: 0.150 AC: 517 AN: 3442

South Asian (SAS) AF: 0.168 AC: 432 AN: 2570

European-Finnish (FIN) AF: 0.0491 AC: 288 AN: 5864

Middle Eastern (MID) AF: 0.0926 AC: 20 AN: 216

European-Non Finnish (NFE) AF: 0.0853 AC: 4505 AN: 52787

Other (OTH) AF: 0.0829 AC: 125 AN: 1507

Alfa AF: 0.0834 Hom.: 4120

Bravo AF: 0.0829

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.12
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7054313; hg19: chrX-82270818;