rs12980602

Variant names:

• chr19-39262180-T-C
• rs12980602

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 0.247 in 151,732 control chromosomes in the GnomAD database, including 4,828 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 0.25 (4828 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 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: 0.247 AC: 37474 AN: 151614 Hom.: 4829 Cov.: 30

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.247 AC: 37497 AN: 151732 Hom.: 4828 Cov.: 30 AF XY: 0.244 AC XY: 18084 AN XY: 74162

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.259

Alfa AF: 0.238 Hom.: 3059

Bravo AF: 0.260

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.85
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12980602; hg19: chr19-39752820;