rs4380187

Variant names:

• chr2-184947213-A-C
• rs4380187

Your query was ambiguous. Multiple possible variants found:

• chr2-184947213-A-C
• chr2-184947213-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 0.349 in 147,360 control chromosomes in the GnomAD database, including 10,708 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 0.35 (10708 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.349 AC: 51462 AN: 147282 Hom.: 10713 Cov.: 26

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.336

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.349 AC: 51433 AN: 147360 Hom.: 10708 Cov.: 26 AF XY: 0.346 AC XY: 24742 AN XY: 71534

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.366

Alfa AF: 0.449 Hom.: 17307

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4380187; hg19: chr2-185811940;