Genetic Variant ENST00000648331.1:n.99-11125A>C (chr17-11210815-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648331.1(ENSG00000285541):n.99-11125A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,518 control chromosomes in the GnomAD database, including 39,007 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 0.68 ( 39007 hom., cov: 29)

Consequence

ENSG00000285541
ENST00000648331.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

Publications

5 publications found

Variant links:

Genes affected

ENSG00000285541 (HGNC:):

ENSG00000285541 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 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
ENSG00000285541	ENST00000648331.1 link	n.99-11125A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103283

AN:

151400

Hom.:

39011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.941

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.687

Gnomad FIN

AF:

0.907

Gnomad MID

AF:

0.780

Gnomad NFE

AF:

0.837

Gnomad OTH

AF:

0.689

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

GnomAD4 genome

AF:

0.682

AC:

103289

AN:

151518

Hom.:

39007

Cov.:

AF XY:

0.684

AC XY:

50618

AN XY:

73984

show subpopulations

African (AFR)

AF:

0.336

AC:

13847

AN:

41270

American (AMR)

AF:

0.741

AC:

11278

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.783

AC:

2717

AN:

3468

East Asian (EAS)

AF:

0.647

AC:

3316

AN:

5122

South Asian (SAS)

AF:

0.686

AC:

3277

AN:

4776

European-Finnish (FIN)

AF:

0.907

AC:

9482

AN:

10460

Middle Eastern (MID)

AF:

0.767

AC:

224

AN:

292

European-Non Finnish (NFE)

AF:

0.837

AC:

56851

AN:

67900

Other (OTH)

AF:

0.686

AC:

1443

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1294

2589

3883

5178

6472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

786

1572

2358

3144

3930

<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:

0.785

Hom.:

179233

Bravo

AF:

0.654

Asia WGS

AF:

0.623

AC:

2167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.56

(source)

DANN

Benign

0.77

PhyloP100

-0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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