rs4380187

chr2-184947213-A-Cchr2-184947213-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/exons	MANE	UniProt

Ensembl

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