rs1566929

Positions:

• chr12-116446008-G-A
• chr12-116446008-G-C

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 0.382 in 152,076 control chromosomes in the GnomAD database, including 11,294 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 0.38 (11294 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 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: 0.382 AC: 58094 AN: 151958 Hom.: 11281 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.382 AC: 58135 AN: 152076 Hom.: 11294 Cov.: 33 AF XY: 0.381 AC XY: 28294 AN XY: 74344

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.398

Alfa AF: 0.402 Hom.: 10171

Bravo AF: 0.374

Asia WGS AF: 0.437 AC: 1518 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566929; hg19: chr12-116883813;