rs7054313

Positions:

• chrX-83015810-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 0.085 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 9378 AN: 110382 Hom.: 293 Cov.: 22 AF XY: 0.0809 AC XY: 2642 AN XY: 32672

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

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0843 Hom.: 2824

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7054313; hg19: chrX-82270818;