Genetic Variant ENSG00000226197:n.162+10950T>C (chr9-13564274-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.162+10950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,194 control chromosomes in the GnomAD database, including 2,811 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 0.14 ( 2811 hom., cov: 32)

Consequence

ENSG00000226197
ENST00000664438.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.176

Publications

1 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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.162+10950T>C	intron_variant	Intron 2 of 2
ENSG00000226197	ENST00000840201.1 link	n.338+10950T>C	intron_variant	Intron 3 of 3
ENSG00000226197	ENST00000840202.1 link	n.822+10950T>C	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20609

AN:

152076

Hom.:

2805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0677

Gnomad EAS

AF:

0.685

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.0493

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0475

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.136

AC:

20640

AN:

152194

Hom.:

2811

Cov.:

AF XY:

0.142

AC XY:

10557

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.223

AC:

9269

AN:

41512

American (AMR)

AF:

0.140

AC:

2133

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0677

AC:

235

AN:

3470

East Asian (EAS)

AF:

0.685

AC:

3540

AN:

5168

South Asian (SAS)

AF:

0.293

AC:

1413

AN:

4818

European-Finnish (FIN)

AF:

0.0493

AC:

523

AN:

10618

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0475

AC:

3228

AN:

68008

Other (OTH)

AF:

0.125

AC:

264

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

767

1533

2300

3066

3833

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<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:

0.0877

Hom.:

2021

Bravo

AF:

0.147

Asia WGS

AF:

0.464

AC:

1607

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.9

(source)

DANN

Benign

0.87

PhyloP100

0.18

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