chrX-97839482-C-G

Variant names:

• chrX-97839482-C-G
• rs391745

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 0.2 in 111,007 control chromosomes in the GnomAD database, including 2,797 homozygotes. There are 6,127 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 0.20 (2797 hom., 6127 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.200 AC: 22209 AN: 110956 Hom.: 2793 Cov.: 22

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.0466

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.200 AC: 22247 AN: 111007 Hom.: 2797 Cov.: 22 AF XY: 0.184 AC XY: 6127 AN XY: 33279

African (AFR) AF: 0.467 AC: 14137 AN: 30292

American (AMR) AF: 0.107 AC: 1123 AN: 10521

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 239 AN: 2636

East Asian (EAS) AF: 0.0613 AC: 218 AN: 3555

South Asian (SAS) AF: 0.0828 AC: 216 AN: 2608

European-Finnish (FIN) AF: 0.0707 AC: 424 AN: 5993

Middle Eastern (MID) AF: 0.142 AC: 31 AN: 218

European-Non Finnish (NFE) AF: 0.105 AC: 5555 AN: 52986

Other (OTH) AF: 0.180 AC: 272 AN: 1512

Alfa AF: 0.0479 Hom.: 234

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.073
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs391745; hg19: chrX-97094480;