chr12-68246803-A-C

Variant names:

• chr12-68246803-A-C
• rs1179246

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 0.488 in 152,086 control chromosomes in the GnomAD database, including 18,574 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 0.49 (18574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74080 AN: 151968 Hom.: 18539 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.488 AC: 74172 AN: 152086 Hom.: 18574 Cov.: 32 AF XY: 0.491 AC XY: 36473 AN XY: 74336

African (AFR) AF: 0.580 AC: 24080 AN: 41494

American (AMR) AF: 0.485 AC: 7416 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1987 AN: 3472

East Asian (EAS) AF: 0.516 AC: 2663 AN: 5158

South Asian (SAS) AF: 0.604 AC: 2908 AN: 4812

European-Finnish (FIN) AF: 0.463 AC: 4899 AN: 10588

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28512 AN: 67964

Other (OTH) AF: 0.527 AC: 1114 AN: 2114

Alfa AF: 0.458 Hom.: 21920

Bravo AF: 0.496

Asia WGS AF: 0.595 AC: 2066 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1179246; hg19: chr12-68640583;