rs12611334

Positions:

• chr19-39738769-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;