rs12778366

Variant names:

• chr10-67883321-T-C
• rs12778366

Your query was ambiguous. Multiple possible variants found:

• chr10-67883321-T-C
• chr10-67883321-T-G

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 0.111 in 152,284 control chromosomes in the GnomAD database, including 973 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 0.11 (973 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 72 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 (SAS) allele frequency at 95% confidence interval = 0.138 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: 0.111 AC: 16886 AN: 152166 Hom.: 973 Cov.: 33

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16902 AN: 152284 Hom.: 973 Cov.: 33 AF XY: 0.111 AC XY: 8275 AN XY: 74468

African (AFR) AF: 0.0738 AC: 3067 AN: 41568

American (AMR) AF: 0.140 AC: 2132 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.130 AC: 674 AN: 5188

South Asian (SAS) AF: 0.147 AC: 708 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1077 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8455 AN: 68018

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.118 Hom.: 2172

Bravo AF: 0.110

Asia WGS AF: 0.126 AC: 438 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	11
DANN	Benign	0.54
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12778366; hg19: chr10-69643079;