X-859245-G-A

Variant names:

• chrX-859245-G-A
• rs35841281

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 0.0864 in 152,146 control chromosomes in the GnomAD database, including 760 homozygotes. There are 6,124 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 0.086 (760 hom., 6124 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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: 0.0865 AC: 13152 AN: 152028 Hom.: 760 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0864 AC: 13151 AN: 152146 Hom.: 760 Cov.: 32 AF XY: 0.0824 AC XY: 6124 AN XY: 74352

African (AFR) AF: 0.0219 AC: 911 AN: 41540

American (AMR) AF: 0.0742 AC: 1133 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3466

East Asian (EAS) AF: 0.0404 AC: 209 AN: 5168

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4822

European-Finnish (FIN) AF: 0.0823 AC: 872 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9261 AN: 67962

Other (OTH) AF: 0.0884 AC: 187 AN: 2116

Bravo AF: 0.0844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs35841281; hg19: chrX-819980;