Genetic Variant ENSG00000291111:n.430-10509G>C (chr6-33130612-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000782892.1(ENSG00000291111):n.430-10509G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,172 control chromosomes in the GnomAD database, including 6,038 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 0.27 ( 6038 hom., cov: 32)

Consequence

ENSG00000291111
ENST00000782892.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.324

Publications

13 publications found

Variant links:

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000291111 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1 link	n.*135C>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291111	ENST00000782892.1 link	n.430-10509G>C	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1 link	n.404-10509G>C	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782894.1 link	n.229-633G>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40682

AN:

152054

Hom.:

6040

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.443

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.266

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

GnomAD4 genome

AF:

0.267

AC:

40687

AN:

152172

Hom.:

6038

Cov.:

AF XY:

0.268

AC XY:

19919

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.147

AC:

6126

AN:

41540

American (AMR)

AF:

0.246

AC:

3766

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

1537

AN:

3472

East Asian (EAS)

AF:

0.385

AC:

1995

AN:

5180

South Asian (SAS)

AF:

0.317

AC:

1525

AN:

4816

European-Finnish (FIN)

AF:

0.331

AC:

3502

AN:

10574

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21434

AN:

67980

Other (OTH)

AF:

0.264

AC:

558

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1511

3022

4534

6045

7556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.314

Hom.:

4304

Bravo

AF:

0.254

Asia WGS

AF:

0.349

AC:

1217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

7.7

(source)

DANN

Benign

0.69

PhyloP100

0.32

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