Genetic Variant ENST00000830683.1:n.137-7276C>T (chr11-44419420-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000830683.1(ENSG00000308049):n.137-7276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,114 control chromosomes in the GnomAD database, including 4,856 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 0.24 ( 4856 hom., cov: 32)

Consequence

ENSG00000308049
ENST00000830683.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500

Publications

3 publications found

Variant links:

Genes affected

ENSG00000308049 (HGNC:):

ENSG00000308049 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 (AMR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000308049	ENST00000830683.1 link	n.137-7276C>T	intron_variant	Intron 1 of 1
ENSG00000308049	ENST00000830684.1 link	n.221-7276C>T	intron_variant	Intron 2 of 2
ENSG00000308049	ENST00000830685.1 link	n.155-7276C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37177

AN:

151996

Hom.:

4830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.264

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

GnomAD4 genome

AF:

0.245

AC:

37248

AN:

152114

Hom.:

4856

Cov.:

AF XY:

0.245

AC XY:

18205

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.210

AC:

8704

AN:

41512

American (AMR)

AF:

0.363

AC:

5550

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

862

AN:

3468

East Asian (EAS)

AF:

0.189

AC:

978

AN:

5164

South Asian (SAS)

AF:

0.160

AC:

770

AN:

4810

European-Finnish (FIN)

AF:

0.192

AC:

2030

AN:

10590

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.258

AC:

17511

AN:

67968

Other (OTH)

AF:

0.261

AC:

551

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1429

2859

4288

5718

7147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.254

Hom.:

21054

Bravo

AF:

0.255

Asia WGS

AF:

0.197

AC:

687

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

1.6

(source)

DANN

Benign

0.71

PhyloP100

-0.0050

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