Genetic Variant ENST00000587140.5:n.193-313C>T (chr19-28375689-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 ENST00000587140.5(ENSG00000267320):n.193-313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,998 control chromosomes in the GnomAD database, including 31,035 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 0.62 ( 31035 hom., cov: 32)

Consequence

ENSG00000267320
ENST00000587140.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.393

Publications

8 publications found

Variant links:

Genes affected

ENSG00000267320 (HGNC:):

ENSG00000267320 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000267320	ENST00000587140.5 link	n.193-313C>T	intron_variant	Intron 2 of 4	5
ENSG00000267320	ENST00000591926.1 link	n.160-313C>T	intron_variant	Intron 2 of 3	4
ENSG00000267320	ENST00000592311.5 link	n.167-313C>T	intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.619

AC:

93939

AN:

151880

Hom.:

31027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.732

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.637

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

GnomAD4 genome

AF:

0.618

AC:

93962

AN:

151998

Hom.:

31035

Cov.:

AF XY:

0.622

AC XY:

46225

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.386

AC:

15963

AN:

41408

American (AMR)

AF:

0.620

AC:

9463

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.714

AC:

2478

AN:

3472

East Asian (EAS)

AF:

0.497

AC:

2569

AN:

5170

South Asian (SAS)

AF:

0.652

AC:

3141

AN:

4814

European-Finnish (FIN)

AF:

0.775

AC:

8202

AN:

10580

Middle Eastern (MID)

AF:

0.680

AC:

200

AN:

294

European-Non Finnish (NFE)

AF:

0.735

AC:

49934

AN:

67964

Other (OTH)

AF:

0.637

AC:

1346

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1668

3335

5003

6670

8338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.684

Hom.:

106662

Bravo

AF:

0.594

Asia WGS

AF:

0.533

AC:

1856

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.43

(source)

DANN

Benign

0.45

PhyloP100

-0.39

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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