12-116889787-T-C

Variant names:

• chr12-116889787-T-C
• rs7294919
• ENST00000752207.1:n.111+11019T>C

Variant summary

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

The ENST00000752207.1(ENSG00000297968):​n.111+11019T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,062 control chromosomes in the GnomAD database, including 3,701 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 0.18 (3701 hom., cov: 32)
• Consequence: ENSG00000297968 ENST00000752207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 78 publications found

Genes affected

ENSG00000297968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752207.1. 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
	ENSG00000297968	ENST00000752207.1		n.111+11019T>C		intron	N/A
	ENSG00000297968	ENST00000752208.1		n.164+2110T>C		intron	N/A
	ENSG00000297968	ENST00000752209.1		n.84-3948T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27792 AN: 151944 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 27835 AN: 152062 Hom.: 3701 Cov.: 32 AF XY: 0.179 AC XY: 13323 AN XY: 74348

African (AFR) AF: 0.378 AC: 15672 AN: 41448

American (AMR) AF: 0.130 AC: 1985 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1044 AN: 5166

South Asian (SAS) AF: 0.0854 AC: 412 AN: 4822

European-Finnish (FIN) AF: 0.0764 AC: 808 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0978 AC: 6651 AN: 68000

Other (OTH) AF: 0.188 AC: 396 AN: 2108

Alfa AF: 0.128 Hom.: 7215

Bravo AF: 0.198

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.66
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7294919; hg19: chr12-117327592;