rs10878640

Variant names:

• chr12-67643308-G-T
• rs10878640

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 0.316 in 152,100 control chromosomes in the GnomAD database, including 7,866 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 0.32 (7866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 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: 0.316 AC: 48066 AN: 151980 Hom.: 7852 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.316 AC: 48104 AN: 152100 Hom.: 7866 Cov.: 32 AF XY: 0.322 AC XY: 23916 AN XY: 74366

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.295

Alfa AF: 0.326 Hom.: 4822

Bravo AF: 0.309

Asia WGS AF: 0.289 AC: 1009 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	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10878640; hg19: chr12-68037088;