rs12980602

Variant names:

• chr19-39262180-T-C
• rs12980602

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 0.247 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.285 AC: 11798 AN: 41358

American (AMR) AF: 0.317 AC: 4826 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3464

East Asian (EAS) AF: 0.108 AC: 560 AN: 5164

South Asian (SAS) AF: 0.254 AC: 1217 AN: 4792

European-Finnish (FIN) AF: 0.178 AC: 1876 AN: 10510

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.232 AC: 15782 AN: 67920

Other (OTH) AF: 0.259 AC: 543 AN: 2094

Alfa AF: 0.236 Hom.: 9796

Bravo AF: 0.260

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.85
DANN	Benign	0.47
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12980602; hg19: chr19-39752820;