rs1026788

Variant names:

• chr12-68257701-T-C
• rs1026788

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 0.54 in 151,884 control chromosomes in the GnomAD database, including 22,399 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 0.54 (22399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 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: 0.540 AC: 81982 AN: 151768 Hom.: 22393 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.540 AC: 82018 AN: 151884 Hom.: 22399 Cov.: 31 AF XY: 0.536 AC XY: 39760 AN XY: 74222

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.494

Alfa AF: 0.576 Hom.: 3155

Bravo AF: 0.536

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1026788; hg19: chr12-68651481;