rs1026788

Variant names:

• chr12-68257701-T-C
• rs1026788

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 0.54 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.520 AC: 21511 AN: 41396

American (AMR) AF: 0.522 AC: 7974 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5154

South Asian (SAS) AF: 0.392 AC: 1889 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5625 AN: 10530

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.580 AC: 39410 AN: 67944

Other (OTH) AF: 0.494 AC: 1041 AN: 2108

Alfa AF: 0.574 Hom.: 3259

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1026788; hg19: chr12-68651481;