Genetic Variant ENSG00000301530:n.138+12470T>C (chr11-69208652-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 ENST00000779509.1(ENSG00000301530):n.138+12470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,054 control chromosomes in the GnomAD database, including 32,648 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 0.65 ( 32648 hom., cov: 32)

Consequence

ENSG00000301530
ENST00000779509.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.84

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301530 (HGNC:):

ENSG00000301530 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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
ENSG00000301530	ENST00000779509.1 link	n.138+12470T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.650

AC:

98723

AN:

151936

Hom.:

32611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.762

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.662

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

GnomAD4 genome

AF:

0.650

AC:

98816

AN:

152054

Hom.:

32648

Cov.:

AF XY:

0.649

AC XY:

48276

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.762

AC:

31605

AN:

41480

American (AMR)

AF:

0.548

AC:

8370

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.735

AC:

2551

AN:

3470

East Asian (EAS)

AF:

0.460

AC:

2373

AN:

5160

South Asian (SAS)

AF:

0.546

AC:

2630

AN:

4814

European-Finnish (FIN)

AF:

0.667

AC:

7051

AN:

10572

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42166

AN:

67962

Other (OTH)

AF:

0.661

AC:

1399

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.616

Hom.:

5734

Bravo

AF:

0.649

Asia WGS

AF:

0.589

AC:

2047

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.095

(source)

DANN

Benign

0.19

PhyloP100

-2.8

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