14-54837343-G-A

Variant names:

• chr14-54837343-G-A
• rs2057369

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 0.224 in 151,752 control chromosomes in the GnomAD database, including 3,918 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 0.22 (3918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.224 AC: 33941 AN: 151634 Hom.: 3910 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.224 AC: 33987 AN: 151752 Hom.: 3918 Cov.: 31 AF XY: 0.227 AC XY: 16801 AN XY: 74124

African (AFR) AF: 0.227 AC: 9367 AN: 41352

American (AMR) AF: 0.297 AC: 4527 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1832 AN: 5160

South Asian (SAS) AF: 0.137 AC: 663 AN: 4822

European-Finnish (FIN) AF: 0.246 AC: 2570 AN: 10452

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13746 AN: 67942

Other (OTH) AF: 0.220 AC: 462 AN: 2104

Alfa AF: 0.211 Hom.: 2062

Bravo AF: 0.231

Asia WGS AF: 0.202 AC: 703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-0.64

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2057369; hg19: chr14-55304061;