rs4026608

chr12-66000884-C-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 0.617 in 151,178 control chromosomes in the GnomAD database, including 29,420 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 0.62 (29420 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.617 AC: 93251 AN: 151058 Hom.: 29384 Cov.: 27

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.617 AC: 93344 AN: 151178 Hom.: 29420 Cov.: 27 AF XY: 0.615 AC XY: 45410 AN XY: 73836

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.600

Alfa AF: 0.605 Hom.: 35502

Bravo AF: 0.605

Asia WGS AF: 0.427 AC: 1485 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.28
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4026608; hg19: chr12-66394664;