ENST00000813240.1:n.192T>C

Variant names:

• chr12-76004953-T-C
• rs2367446
• ENST00000813240.1:n.192T>C

Variant summary

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

The ENST00000813240.1(ENSG00000257329):​n.192T>C 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 0.277 in 152,108 control chromosomes in the GnomAD database, including 6,793 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 0.28 (6793 hom., cov: 32)
• Consequence: ENSG00000257329 ENST00000813240.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 5 publications found

Genes affected

ENSG00000257329 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813240.1. 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
	ENSG00000257329	ENST00000813240.1		n.192T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000305824	ENST00000813167.1		n.183+1236A>G		intron	N/A
	ENSG00000305824	ENST00000813168.1		n.267+1236A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42081 AN: 151990 Hom.: 6795 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.277 AC: 42061 AN: 152108 Hom.: 6793 Cov.: 32 AF XY: 0.282 AC XY: 20985 AN XY: 74342

African (AFR) AF: 0.113 AC: 4674 AN: 41512

American (AMR) AF: 0.274 AC: 4182 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2475 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4237 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23122 AN: 67990

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.317 Hom.: 6576

Bravo AF: 0.260

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.031
DANN	Benign	0.47
PhyloP100		-1.6

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: rs2367446;

hg19: chr12-76398733;