rs10778699

Positions:

• chr12-80069304-G-A

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 0.28 in 151,932 control chromosomes in the GnomAD database, including 6,101 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 (6101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42533 AN: 151816 Hom.: 6098 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.280 AC: 42554 AN: 151932 Hom.: 6101 Cov.: 32 AF XY: 0.278 AC XY: 20623 AN XY: 74272

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.306

Alfa AF: 0.308 Hom.: 6853

Bravo AF: 0.277

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.15
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778699; hg19: chr12-80463084;