rs10521667

Positions:

• chrX-7897454-C-T

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 0.0694 in 111,791 control chromosomes in the GnomAD database, including 649 homozygotes. There are 2,086 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 0.069 (649 hom., 2086 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7897454C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 7752 AN: 111739 Hom.: 648 Cov.: 23 AF XY: 0.0614 AC XY: 2087 AN XY: 33981

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.00641

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00183

Gnomad FIN AF: 0.000166

Gnomad MID AF: 0.0208

Gnomad NFE AF: 0.000770

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0694 AC: 7755 AN: 111791 Hom.: 649 Cov.: 23 AF XY: 0.0613 AC XY: 2086 AN XY: 34045

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0293

Gnomad4 ASJ AF: 0.00641

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00183

Gnomad4 FIN AF: 0.000166

Gnomad4 NFE AF: 0.000770

Gnomad4 OTH AF: 0.0505

Alfa AF: 0.0546 Hom.: 202

Bravo AF: 0.0807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521667; hg19: chrX-7865495;