rs12611334

Variant names:

• chr19-39738769-C-G
• rs12611334

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 0.279 in 152,156 control chromosomes in the GnomAD database, including 6,343 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 0.28 (6343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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: 0.279 AC: 42459 AN: 152038 Hom.: 6341 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.279 AC: 42465 AN: 152156 Hom.: 6343 Cov.: 32 AF XY: 0.277 AC XY: 20613 AN XY: 74384

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.241

Alfa AF: 0.325 Hom.: 1073

Bravo AF: 0.261

Asia WGS AF: 0.226 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12611334; hg19: chr19-40229409;