rs11067829

chr12-109679067-A-Gchr12-109679067-A-T

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 0.233 in 152,034 control chromosomes in the GnomAD database, including 4,805 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 0.23 (4805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.233 AC: 35428 AN: 151916 Hom.: 4804 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.233 AC: 35447 AN: 152034 Hom.: 4805 Cov.: 32 AF XY: 0.243 AC XY: 18069 AN XY: 74324

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.255

Alfa AF: 0.209 Hom.: 614

Bravo AF: 0.243

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	13
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: rs11067829; hg19: chr12-110116872;