X-98435234-C-A

Variant names:

• chrX-98435234-C-A
• rs6616002

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 0.305 in 111,200 control chromosomes in the GnomAD database, including 4,061 homozygotes. There are 10,364 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 0.31 (4061 hom., 10364 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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: 0.305 AC: 33935 AN: 111148 Hom.: 4069 Cov.: 23

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.305 AC: 33929 AN: 111200 Hom.: 4061 Cov.: 23 AF XY: 0.309 AC XY: 10364 AN XY: 33498

African (AFR) AF: 0.197 AC: 6049 AN: 30730

American (AMR) AF: 0.469 AC: 4891 AN: 10432

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 996 AN: 2632

East Asian (EAS) AF: 0.708 AC: 2494 AN: 3521

South Asian (SAS) AF: 0.544 AC: 1467 AN: 2698

European-Finnish (FIN) AF: 0.220 AC: 1305 AN: 5927

Middle Eastern (MID) AF: 0.295 AC: 64 AN: 217

European-Non Finnish (NFE) AF: 0.303 AC: 16014 AN: 52840

Other (OTH) AF: 0.346 AC: 529 AN: 1530

Alfa AF: 0.305 Hom.: 16889

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs6616002; hg19: chrX-97690232;