rs10778699

Variant names:

• chr12-80069304-G-A
• rs10778699

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.234 AC: 9670 AN: 41408

American (AMR) AF: 0.247 AC: 3772 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1561 AN: 5154

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2610 AN: 10554

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21606 AN: 67956

Other (OTH) AF: 0.306 AC: 645 AN: 2110

Alfa AF: 0.301 Hom.: 19313

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10778699; hg19: chr12-80463084;