14-90204794-A-G

Variant names:

• chr14-90204794-A-G
• rs769044

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 151,964 control chromosomes in the GnomAD database, including 22,734 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 (22734 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.909
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81047 AN: 151846 Hom.: 22725 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.534 AC: 81082 AN: 151964 Hom.: 22734 Cov.: 31 AF XY: 0.535 AC XY: 39714 AN XY: 74282

African (AFR) AF: 0.358 AC: 14846 AN: 41452

American (AMR) AF: 0.603 AC: 9201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2371 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2454 AN: 5156

South Asian (SAS) AF: 0.622 AC: 2992 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6238 AN: 10530

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

European-Non Finnish (NFE) AF: 0.606 AC: 41151 AN: 67958

Other (OTH) AF: 0.576 AC: 1217 AN: 2112

Alfa AF: 0.585 Hom.: 13466

Bravo AF: 0.524

Asia WGS AF: 0.561 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.68
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs769044; hg19: chr14-90671138;