rs10878640

Positions:

• chr12-67643308-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;