rs2384550

Variant names:

• chr12-114914926-G-A
• rs2384550

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 0.328 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.350

Alfa AF: 0.347 Hom.: 22262

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2384550; hg19: chr12-115352731;