rs1026788

Positions:

• chr12-68257701-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;