chrX-146163912-T-C

Variant names:

• chrX-146163912-T-C
• rs9306713

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 0.19 in 110,929 control chromosomes in the GnomAD database, including 1,975 homozygotes. There are 5,794 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 0.19 (1975 hom., 5794 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.189 AC: 20980 AN: 110874 Hom.: 1974 Cov.: 22

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0634

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00705

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.190 AC: 21023 AN: 110929 Hom.: 1975 Cov.: 22 AF XY: 0.175 AC XY: 5794 AN XY: 33163

African (AFR) AF: 0.355 AC: 10775 AN: 30374

American (AMR) AF: 0.105 AC: 1092 AN: 10428

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 348 AN: 2637

East Asian (EAS) AF: 0.00707 AC: 25 AN: 3536

South Asian (SAS) AF: 0.0744 AC: 196 AN: 2633

European-Finnish (FIN) AF: 0.118 AC: 701 AN: 5930

Middle Eastern (MID) AF: 0.119 AC: 26 AN: 218

European-Non Finnish (NFE) AF: 0.142 AC: 7548 AN: 52988

Other (OTH) AF: 0.178 AC: 269 AN: 1507

Alfa AF: 0.159 Hom.: 10081

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9306713; hg19: chrX-145245430;