rs1402078

chrX-93262662-A-GchrX-93262662-A-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 0.217 in 110,051 control chromosomes in the GnomAD database, including 3,034 homozygotes. There are 6,593 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 0.22 (3034 hom., 6593 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 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: 0.217 AC: 23882 AN: 110000 Hom.: 3032 Cov.: 21 AF XY: 0.203 AC XY: 6556 AN XY: 32316

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0367

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.217 AC: 23926 AN: 110051 Hom.: 3034 Cov.: 21 AF XY: 0.204 AC XY: 6593 AN XY: 32377

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.187

Alfa AF: 0.128 Hom.: 6328

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402078; hg19: chrX-92517661;