rs10778536

Variant names:

• chr12-107136216-G-A
• rs10778536

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 0.608 in 152,046 control chromosomes in the GnomAD database, including 28,429 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 0.61 (28429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.608 AC: 92295 AN: 151926 Hom.: 28401 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.608 AC: 92374 AN: 152046 Hom.: 28429 Cov.: 32 AF XY: 0.613 AC XY: 45508 AN XY: 74292

African (AFR) AF: 0.543 AC: 22531 AN: 41466

American (AMR) AF: 0.618 AC: 9454 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4862 AN: 5166

South Asian (SAS) AF: 0.584 AC: 2813 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6913 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42175 AN: 67960

Other (OTH) AF: 0.602 AC: 1270 AN: 2110

Alfa AF: 0.616 Hom.: 117997

Bravo AF: 0.604

Asia WGS AF: 0.731 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10778536; hg19: chr12-107529994;