2-57714152-A-G

Variant names:

• chr2-57714152-A-G
• rs1380703

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 0.314 in 152,116 control chromosomes in the GnomAD database, including 8,677 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 0.31 (8677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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: 0.314 AC: 47800 AN: 151998 Hom.: 8674 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.314 AC: 47818 AN: 152116 Hom.: 8677 Cov.: 32 AF XY: 0.320 AC XY: 23781 AN XY: 74346

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.360

Alfa AF: 0.343 Hom.: 5669

Bravo AF: 0.303

Asia WGS AF: 0.516 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380703; hg19: chr2-57941287;