rs13384439

Variant names:

• chr2-186927134-A-G
• rs13384439

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 0.261 in 151,970 control chromosomes in the GnomAD database, including 5,726 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 0.26 (5726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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: 0.261 AC: 39631 AN: 151850 Hom.: 5729 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39651 AN: 151970 Hom.: 5726 Cov.: 31 AF XY: 0.260 AC XY: 19357 AN XY: 74308

African (AFR) AF: 0.356 AC: 14763 AN: 41416

American (AMR) AF: 0.337 AC: 5138 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3464

East Asian (EAS) AF: 0.171 AC: 882 AN: 5160

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10582

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14150 AN: 67960

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.229 Hom.: 2875

Bravo AF: 0.278

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs13384439; hg19: chr2-187791861;