rs2057368

Variant names:

• chr14-54837291-G-A
• rs2057368

Your query was ambiguous. Multiple possible variants found:

• chr14-54837291-G-A
• chr14-54837291-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.215

Alfa AF: 0.187 Hom.: 4074

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057368; hg19: chr14-55304009;