Genetic Variant ENSG00000305635:n.328-2343T>A (chr19-48952668-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000812088.1(ENSG00000305635):n.328-2343T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,234 control chromosomes in the GnomAD database, including 60,940 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 0.89 ( 60940 hom., cov: 32)

Consequence

ENSG00000305635
ENST00000812088.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120

Publications

10 publications found

Variant links:

Genes affected

ENSG00000305635 (HGNC:):

ENSG00000305635 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000305635	ENST00000812088.1 link	n.328-2343T>A	intron_variant	Intron 1 of 1
ENSG00000305635	ENST00000812089.1 link	n.472-2343T>A	intron_variant	Intron 2 of 2
ENSG00000305635	ENST00000812090.1 link	n.273-2343T>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.894

AC:

136020

AN:

152116

Hom.:

60889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.913

Gnomad AMI

AF:

0.790

Gnomad AMR

AF:

0.844

Gnomad ASJ

AF:

0.914

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.951

Gnomad FIN

AF:

0.922

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.882

Gnomad OTH

AF:

0.876

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

GnomAD4 genome

AF:

0.894

AC:

136130

AN:

152234

Hom.:

60940

Cov.:

AF XY:

0.897

AC XY:

66718

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.913

AC:

37904

AN:

41536

American (AMR)

AF:

0.844

AC:

12892

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.914

AC:

3173

AN:

3472

East Asian (EAS)

AF:

0.952

AC:

4925

AN:

5176

South Asian (SAS)

AF:

0.951

AC:

4596

AN:

4832

European-Finnish (FIN)

AF:

0.922

AC:

9777

AN:

10602

Middle Eastern (MID)

AF:

0.918

AC:

270

AN:

294

European-Non Finnish (NFE)

AF:

0.882

AC:

60023

AN:

68026

Other (OTH)

AF:

0.877

AC:

1853

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

750

1500

2249

2999

3749

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.892

Hom.:

7520

Bravo

AF:

0.887

Asia WGS

AF:

0.915

AC:

3184

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

0.36

(source)

DANN

Benign

0.63

PhyloP100

-0.012

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