rs12789493

Variant names:

• chr11-76564659-T-C
• rs12789493
• ENST00000830356.1:n.398+8682A>G

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.398+8682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,918 control chromosomes in the GnomAD database, including 23,940 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 0.56 (23940 hom., cov: 31)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 9 publications found

Genes affected

ENSG00000308001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830356.1. 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
	ENSG00000308001	ENST00000830356.1		n.398+8682A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85034 AN: 151800 Hom.: 23931 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.560 AC: 85083 AN: 151918 Hom.: 23940 Cov.: 31 AF XY: 0.557 AC XY: 41357 AN XY: 74272

African (AFR) AF: 0.553 AC: 22893 AN: 41412

American (AMR) AF: 0.498 AC: 7589 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2591 AN: 5168

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6056 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39235 AN: 67946

Other (OTH) AF: 0.569 AC: 1200 AN: 2110

Alfa AF: 0.571 Hom.: 92669

Bravo AF: 0.557

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12789493;

hg19: chr11-76275703;