rs12980971

Variant names:

• chr19-51677673-C-G
• rs12980971

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 0.652 in 151,624 control chromosomes in the GnomAD database, including 33,618 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 0.65 (33618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.651 AC: 98698 AN: 151508 Hom.: 33585 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.652 AC: 98788 AN: 151624 Hom.: 33618 Cov.: 32 AF XY: 0.648 AC XY: 47992 AN XY: 74028

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.616

Alfa AF: 0.625 Hom.: 3818

Bravo AF: 0.660

Asia WGS AF: 0.403 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12980971; hg19: chr19-52180926;