rs12972991

Variant names:

• chr19-39241107-A-C
• rs12972991

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 0.195 in 152,126 control chromosomes in the GnomAD database, including 3,335 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 0.20 (3335 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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: 0.195 AC: 29671 AN: 152010 Hom.: 3336 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.195 AC: 29678 AN: 152126 Hom.: 3335 Cov.: 31 AF XY: 0.191 AC XY: 14241 AN XY: 74388

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0623

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.210

Alfa AF: 0.239 Hom.: 6637

Bravo AF: 0.202

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12972991; hg19: chr19-39731747;