rs10878378

Variant names:

• chr12-66105732-T-A
• rs10878378

Your query was ambiguous. Multiple possible variants found:

• chr12-66105732-T-A
• chr12-66105732-T-C
• chr12-66105732-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 0.515 in 152,096 control chromosomes in the GnomAD database, including 21,600 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 0.52 (21600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• 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 = 0.839 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78264 AN: 151978 Hom.: 21563 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.515 AC: 78354 AN: 152096 Hom.: 21600 Cov.: 33 AF XY: 0.519 AC XY: 38557 AN XY: 74338

African (AFR) AF: 0.668 AC: 27712 AN: 41460

American (AMR) AF: 0.368 AC: 5623 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1789 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4464 AN: 5188

South Asian (SAS) AF: 0.571 AC: 2756 AN: 4828

European-Finnish (FIN) AF: 0.486 AC: 5140 AN: 10576

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29424 AN: 67980

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.286 Hom.: 613

Bravo AF: 0.513

Asia WGS AF: 0.679 AC: 2361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.73
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10878378; hg19: chr12-66499512;