rs1402078

Variant names:

• chrX-93262662-A-G
• rs1402078

Your query was ambiguous. Multiple possible variants found:

• chrX-93262662-A-G
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;