rs12980275

Variant names:

• chr19-39241143-A-G
• rs12980275

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 0.355 in 151,908 control chromosomes in the GnomAD database, including 10,661 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 0.36 (10661 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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: 0.355 AC: 53870 AN: 151790 Hom.: 10634 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.355 AC: 53945 AN: 151908 Hom.: 10661 Cov.: 31 AF XY: 0.347 AC XY: 25799 AN XY: 74254

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.337

Alfa AF: 0.316 Hom.: 18084

Bravo AF: 0.374

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12980275; hg19: chr19-39731783;