rs1380703

Positions:

• chr2-57714152-A-G
• chr2-57714152-A-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;