14-55482908-A-G

Variant names:

• chr14-55482908-A-G
• rs12433615

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 0.286 in 152,102 control chromosomes in the GnomAD database, including 7,357 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 0.29 (7357 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43463 AN: 151984 Hom.: 7346 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.286 AC: 43497 AN: 152102 Hom.: 7357 Cov.: 33 AF XY: 0.297 AC XY: 22063 AN XY: 74344

African (AFR) AF: 0.108 AC: 4475 AN: 41520

American (AMR) AF: 0.346 AC: 5289 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2420 AN: 5180

South Asian (SAS) AF: 0.485 AC: 2339 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4722 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22361 AN: 67964

Other (OTH) AF: 0.293 AC: 620 AN: 2114

Alfa AF: 0.305 Hom.: 1401

Bravo AF: 0.274

Asia WGS AF: 0.479 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.72
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs12433615; hg19: chr14-55949626;