chr12-66268223-C-T

Variant names:

• chr12-66268223-C-T
• rs289068
• ENST00000767942.1:n.97+318G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000767942.1(ENSG00000300010):​n.97+318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,974 control chromosomes in the GnomAD database, including 44,692 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 0.77 (44692 hom., cov: 30)
• Consequence: ENSG00000300010 ENST00000767942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 publications found

Genes affected

ENSG00000300010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767942.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000300010	ENST00000767942.1		n.97+318G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116532 AN: 151856 Hom.: 44646 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.767 AC: 116637 AN: 151974 Hom.: 44692 Cov.: 30 AF XY: 0.772 AC XY: 57307 AN XY: 74264

African (AFR) AF: 0.767 AC: 31752 AN: 41394

American (AMR) AF: 0.815 AC: 12457 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4275 AN: 5180

South Asian (SAS) AF: 0.823 AC: 3961 AN: 4814

European-Finnish (FIN) AF: 0.775 AC: 8175 AN: 10544

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50799 AN: 67966

Other (OTH) AF: 0.766 AC: 1616 AN: 2110

Alfa AF: 0.760 Hom.: 17026

Bravo AF: 0.769

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.57
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs289068; hg19: chr12-66662003;