Genetic Variant ENSG00000307533:n.*193T>C (chr10-119206827-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 ENST00000826909.1(ENSG00000307533):n.*193T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.995 in 151,916 control chromosomes in the GnomAD database, including 75,172 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 0.99 ( 75172 hom., cov: 32)

Consequence

ENSG00000307533
ENST00000826909.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

9 publications found

Variant links:

Genes affected

ENSG00000307533 (HGNC:):

ENSG00000307533 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 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
ENSG00000307533	ENST00000826909.1 link	n.*193T>C		downstream_gene_variant
ENSG00000307533	ENST00000826910.1 link	n.*193T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.995

AC:

151013

AN:

151804

Hom.:

75119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.982

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.998

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.998

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

GnomAD4 genome

AF:

0.995

AC:

151122

AN:

151916

Hom.:

75172

Cov.:

AF XY:

0.995

AC XY:

73897

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.982

AC:

40776

AN:

41520

American (AMR)

AF:

0.998

AC:

15240

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3470

AN:

3470

East Asian (EAS)

AF:

1.00

AC:

5152

AN:

5152

South Asian (SAS)

AF:

1.00

AC:

4830

AN:

4830

European-Finnish (FIN)

AF:

1.00

AC:

10470

AN:

10470

Middle Eastern (MID)

AF:

0.997

AC:

291

AN:

292

European-Non Finnish (NFE)

AF:

1.00

AC:

67877

AN:

67888

Other (OTH)

AF:

0.998

AC:

2104

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

130

174

217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

914

1828

2742

3656

4570

<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:

0.998

Hom.:

73435

Bravo

AF:

0.994

Asia WGS

AF:

0.999

AC:

3474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.39

(source)

DANN

Benign

0.22

PhyloP100

-1.5

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