X-93262662-A-G

Variant names:

• chrX-93262662-A-G
• rs1402078

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 0.217 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.217 AC: 23882 AN: 110000 Hom.: 3032 Cov.: 21

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

African (AFR) AF: 0.482 AC: 14493 AN: 30089

American (AMR) AF: 0.123 AC: 1271 AN: 10308

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 295 AN: 2631

East Asian (EAS) AF: 0.0193 AC: 67 AN: 3477

South Asian (SAS) AF: 0.155 AC: 397 AN: 2568

European-Finnish (FIN) AF: 0.0943 AC: 552 AN: 5851

Middle Eastern (MID) AF: 0.124 AC: 27 AN: 217

European-Non Finnish (NFE) AF: 0.124 AC: 6522 AN: 52746

Other (OTH) AF: 0.187 AC: 277 AN: 1483

Alfa AF: 0.148 Hom.: 10756

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1402078; hg19: chrX-92517661;