Genetic Variant ENST00000535764.1:n.212+9470T>C (chr12-19932726-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 ENST00000535764.1(ENSG00000255910):n.212+9470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,068 control chromosomes in the GnomAD database, including 9,095 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 0.34 ( 9095 hom., cov: 33)

Consequence

ENSG00000255910
ENST00000535764.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.645

Publications

3 publications found

Variant links:

Genes affected

ENSG00000255910 (HGNC:):

ENSG00000255910 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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
ENSG00000255910	ENST00000535764.1 link	n.212+9470T>C	intron_variant	Intron 2 of 4	3
ENSG00000255910	ENST00000716354.1 link	n.315+9470T>C	intron_variant	Intron 2 of 10
ENSG00000255910	ENST00000716355.1 link	n.245+9470T>C	intron_variant	Intron 2 of 12

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51141

AN:

151948

Hom.:

9073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.635

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.342

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

GnomAD4 genome

AF:

0.337

AC:

51210

AN:

152068

Hom.:

9095

Cov.:

AF XY:

0.335

AC XY:

24932

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.393

AC:

16311

AN:

41468

American (AMR)

AF:

0.365

AC:

5573

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1140

AN:

3470

East Asian (EAS)

AF:

0.635

AC:

3275

AN:

5160

South Asian (SAS)

AF:

0.194

AC:

934

AN:

4824

European-Finnish (FIN)

AF:

0.253

AC:

2676

AN:

10580

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20262

AN:

67984

Other (OTH)

AF:

0.347

AC:

730

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1726

3453

5179

6906

8632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.320

Hom.:

15752

Bravo

AF:

0.353

Asia WGS

AF:

0.361

AC:

1258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.65

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