Genetic Variant ENST00000570140.1:n.1498C>T (chr12-275626-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000570140.1(ENSG00000261799):n.1498C>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 0.314 in 151,978 control chromosomes in the GnomAD database, including 8,497 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 0.31 ( 8497 hom., cov: 32)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

ENSG00000261799
ENST00000570140.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.219

Publications

7 publications found

Variant links:

Genes affected

ENSG00000261799 (HGNC:):

ENSG00000261799 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261799	ENST00000570140.1 link	n.1498C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290285	ENST00000703815.1 link	n.623G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47695

AN:

151850

Hom.:

8479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.272

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.700

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.314

AC:

47750

AN:

151968

Hom.:

8497

Cov.:

AF XY:

0.313

AC XY:

23283

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.490

AC:

20277

AN:

41422

American (AMR)

AF:

0.208

AC:

3185

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

695

AN:

3466

East Asian (EAS)

AF:

0.221

AC:

1144

AN:

5170

South Asian (SAS)

AF:

0.305

AC:

1471

AN:

4822

European-Finnish (FIN)

AF:

0.318

AC:

3349

AN:

10542

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.247

AC:

16816

AN:

67952

Other (OTH)

AF:

0.269

AC:

568

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1578

3156

4733

6311

7889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.260

Hom.:

7276

Bravo

AF:

0.314

Asia WGS

AF:

0.272

AC:

945

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.48

(source)

DANN

Benign

0.34

PhyloP100

-0.22

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