14-90213566-T-C

Variant names:

• chr14-90213566-T-C
• rs8017423

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 0.534 in 152,100 control chromosomes in the GnomAD database, including 22,760 homozygotes. 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 0.53 (22760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 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: 0.534 AC: 81113 AN: 151982 Hom.: 22749 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.534 AC: 81155 AN: 152100 Hom.: 22760 Cov.: 32 AF XY: 0.535 AC XY: 39768 AN XY: 74352

African (AFR) AF: 0.358 AC: 14861 AN: 41498

American (AMR) AF: 0.603 AC: 9208 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2373 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2450 AN: 5162

South Asian (SAS) AF: 0.622 AC: 3000 AN: 4822

European-Finnish (FIN) AF: 0.594 AC: 6277 AN: 10576

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41160 AN: 67978

Other (OTH) AF: 0.577 AC: 1214 AN: 2104

Alfa AF: 0.584 Hom.: 90749

Bravo AF: 0.524

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs8017423; hg19: chr14-90679910;