Genetic Variant ENST00000412132.2:n.823C>T (chr6-11811081-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412132.2(ENSG00000234427):n.823C>T 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 0.508 in 152,144 control chromosomes in the GnomAD database, including 22,539 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 0.51 ( 22537 hom., cov: 32)

Exomes 𝑓: 0.37 ( 2 hom. )

Consequence

ENSG00000234427
ENST00000412132.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0890

Publications

9 publications found

Variant links:

Genes affected

ENSG00000234427 (HGNC:):

ENSG00000234427 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986567	XR_001743970.2 link	n.186G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124901257	XR_007059451.1 link	n.*18C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000234427	ENST00000412132.2 link	n.823C>T	non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000234427	ENST00000761720.1 link	n.700C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000234427	ENST00000761721.1 link	n.333C>T	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.507

AC:

77098

AN:

151980

Hom.:

22488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.498

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.370

AC:

AN:

Hom.:

Cov.:

AF XY:

0.467

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.281

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.560

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.508

AC:

77204

AN:

152098

Hom.:

22537

Cov.:

AF XY:

0.513

AC XY:

38135

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.808

AC:

33516

AN:

41504

American (AMR)

AF:

0.487

AC:

7447

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1488

AN:

3468

East Asian (EAS)

AF:

0.497

AC:

2567

AN:

5162

South Asian (SAS)

AF:

0.544

AC:

2622

AN:

4818

European-Finnish (FIN)

AF:

0.454

AC:

4804

AN:

10570

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23331

AN:

67976

Other (OTH)

AF:

0.482

AC:

1018

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1671

3342

5014

6685

8356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.399

Hom.:

9226

Bravo

AF:

0.521

Asia WGS

AF:

0.553

AC:

1927

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

(source)

DANN

Benign

0.35

PhyloP100

0.089

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over