chr14-74622392-A-G

Variant names:

• chr14-74622392-A-G
• rs888419

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 0.411 in 152,154 control chromosomes in the GnomAD database, including 13,900 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 0.41 (13900 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.411 AC: 62483 AN: 152034 Hom.: 13892 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.411 AC: 62517 AN: 152154 Hom.: 13900 Cov.: 33 AF XY: 0.411 AC XY: 30551 AN XY: 74382

African (AFR) AF: 0.269 AC: 11174 AN: 41504

American (AMR) AF: 0.497 AC: 7604 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1735 AN: 3472

East Asian (EAS) AF: 0.134 AC: 695 AN: 5188

South Asian (SAS) AF: 0.338 AC: 1631 AN: 4826

European-Finnish (FIN) AF: 0.448 AC: 4736 AN: 10582

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33441 AN: 67966

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.473 Hom.: 22625

Bravo AF: 0.407

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.45
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs888419; hg19: chr14-75089095;