chr12-110266682-C-T

Variant names:

• chr12-110266682-C-T
• rs11065611
• ENST00000746209.1:n.544G>A

Variant summary

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

The ENST00000746209.1(ENSG00000289311):​n.544G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,322 control chromosomes in the GnomAD database, including 326 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 0.056 (326 hom., cov: 32)
• Consequence: ENSG00000289311 ENST00000746209.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 21 publications found

Genes affected

ENSG00000289311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746209.1. 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
	ENSG00000289311	ENST00000746209.1		n.544G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000289311	ENST00000746208.1		n.1026+13336G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8576 AN: 152204 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0564 AC: 8590 AN: 152322 Hom.: 326 Cov.: 32 AF XY: 0.0571 AC XY: 4255 AN XY: 74476

African (AFR) AF: 0.0138 AC: 575 AN: 41584

American (AMR) AF: 0.0764 AC: 1168 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5192

South Asian (SAS) AF: 0.155 AC: 746 AN: 4826

European-Finnish (FIN) AF: 0.0751 AC: 797 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4973 AN: 68032

Other (OTH) AF: 0.0398 AC: 84 AN: 2112

Alfa AF: 0.0674 Hom.: 1303

Bravo AF: 0.0523

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs11065611; hg19: chr12-110704487;