rs4026608

Variant names:

• chr12-66000884-C-T
• rs4026608

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 0.617 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.683 AC: 28113 AN: 41168

American (AMR) AF: 0.532 AC: 8068 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2250 AN: 3464

East Asian (EAS) AF: 0.219 AC: 1122 AN: 5132

South Asian (SAS) AF: 0.531 AC: 2532 AN: 4764

European-Finnish (FIN) AF: 0.662 AC: 6894 AN: 10410

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42363 AN: 67796

Other (OTH) AF: 0.600 AC: 1254 AN: 2090

Alfa AF: 0.610 Hom.: 89003

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs4026608; hg19: chr12-66394664;