rs2384550

Variant names:

• chr12-114914926-G-A
• rs2384550

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 0.328 in 151,786 control chromosomes in the GnomAD database, including 8,443 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 0.33 (8443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 58 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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: 0.328 AC: 49727 AN: 151666 Hom.: 8438 Cov.: 31

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.328 AC: 49763 AN: 151786 Hom.: 8443 Cov.: 31 AF XY: 0.324 AC XY: 24021 AN XY: 74164

African (AFR) AF: 0.329 AC: 13616 AN: 41382

American (AMR) AF: 0.271 AC: 4132 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1659 AN: 3462

East Asian (EAS) AF: 0.151 AC: 779 AN: 5160

South Asian (SAS) AF: 0.341 AC: 1631 AN: 4778

European-Finnish (FIN) AF: 0.314 AC: 3304 AN: 10524

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23460 AN: 67906

Other (OTH) AF: 0.350 AC: 738 AN: 2110

Alfa AF: 0.342 Hom.: 44442

Bravo AF: 0.325

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.60
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2384550; hg19: chr12-115352731;