Genetic Variant ENSG00000226197:n.163-81120T>C (chr9-13755193-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 ENST00000664438.1(ENSG00000226197):n.163-81120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,942 control chromosomes in the GnomAD database, including 24,475 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 0.55 ( 24475 hom., cov: 31)

Consequence

ENSG00000226197
ENST00000664438.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

Publications

5 publications found

Variant links:

Genes affected

ENSG00000226197 (HGNC:):

ENSG00000226197 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000226197	ENST00000664438.1 link	n.163-81120T>C	intron_variant	Intron 2 of 2
ENSG00000289185	ENST00000741129.1 link	n.1194-42504A>G	intron_variant	Intron 10 of 10
ENSG00000289185	ENST00000741130.1 link	n.1688-15573A>G	intron_variant	Intron 13 of 13

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83765

AN:

151824

Hom.:

24457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.657

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.895

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.653

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.550

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

GnomAD4 genome

AF:

0.552

AC:

83810

AN:

151942

Hom.:

24475

Cov.:

AF XY:

0.559

AC XY:

41497

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.371

AC:

15345

AN:

41414

American (AMR)

AF:

0.607

AC:

9257

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

2108

AN:

3470

East Asian (EAS)

AF:

0.894

AC:

4610

AN:

5156

South Asian (SAS)

AF:

0.746

AC:

3598

AN:

4822

European-Finnish (FIN)

AF:

0.653

AC:

6896

AN:

10562

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.590

AC:

40087

AN:

67948

Other (OTH)

AF:

0.556

AC:

1175

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1816

3631

5447

7262

9078

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.591

Hom.:

15727

Bravo

AF:

0.541

Asia WGS

AF:

0.778

AC:

2702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.23

(source)

DANN

Benign

0.49

PhyloP100

-1.3

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