rs12980602

Positions:

• chr19-39262180-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;