14-54837291-G-A

Variant names:

• chr14-54837291-G-A
• rs2057368

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 0.218 in 151,876 control chromosomes in the GnomAD database, including 3,742 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 (3742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 10 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 = 0.343 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: 0.218 AC: 33032 AN: 151758 Hom.: 3738 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.218 AC: 33066 AN: 151876 Hom.: 3742 Cov.: 32 AF XY: 0.221 AC XY: 16384 AN XY: 74214

African (AFR) AF: 0.204 AC: 8427 AN: 41400

American (AMR) AF: 0.295 AC: 4511 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5164

South Asian (SAS) AF: 0.135 AC: 652 AN: 4814

European-Finnish (FIN) AF: 0.247 AC: 2595 AN: 10492

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13764 AN: 67950

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.199 Hom.: 10574

Bravo AF: 0.224

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2057368; hg19: chr14-55304009;