Genetic Variant ENSG00000308788:n.123+1198T>C (chr17-19900934-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000836360.1(ENSG00000308788):n.123+1198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,892 control chromosomes in the GnomAD database, including 12,877 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 0.40 ( 12877 hom., cov: 32)

Consequence

ENSG00000308788
ENST00000836360.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.600

Publications

35 publications found

Variant links:

Genes affected

ENSG00000308788 (HGNC:):

ENSG00000308788 links:

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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 = 0.498 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
ENSG00000308788	ENST00000836360.1 link	n.123+1198T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61398

AN:

151774

Hom.:

12863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.405

AC:

61466

AN:

151892

Hom.:

12877

Cov.:

AF XY:

0.402

AC XY:

29829

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.504

AC:

20874

AN:

41406

American (AMR)

AF:

0.423

AC:

6451

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

1283

AN:

3472

East Asian (EAS)

AF:

0.189

AC:

972

AN:

5154

South Asian (SAS)

AF:

0.287

AC:

1380

AN:

4810

European-Finnish (FIN)

AF:

0.349

AC:

3682

AN:

10556

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25553

AN:

67932

Other (OTH)

AF:

0.391

AC:

824

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1867

3734

5601

7468

9335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.385

Hom.:

49517

Bravo

AF:

0.417

Asia WGS

AF:

0.234

AC:

817

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

1.0

(source)

DANN

Benign

0.77

PhyloP100

-0.60

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