chr2-184947213-A-C

Variant names:

• chr2-184947213-A-C
• rs4380187

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.104 AC: 4133 AN: 39740

American (AMR) AF: 0.398 AC: 5919 AN: 14870

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1708 AN: 3440

East Asian (EAS) AF: 0.433 AC: 2171 AN: 5014

South Asian (SAS) AF: 0.402 AC: 1880 AN: 4680

European-Finnish (FIN) AF: 0.383 AC: 3531 AN: 9216

Middle Eastern (MID) AF: 0.332 AC: 93 AN: 280

European-Non Finnish (NFE) AF: 0.459 AC: 30861 AN: 67192

Other (OTH) AF: 0.366 AC: 741 AN: 2022

Alfa AF: 0.447 Hom.: 19722

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4380187; hg19: chr2-185811940;