Genetic Variant ENSG00000305475:n.459-8185T>C (chr10-84044676-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000811232.1(ENSG00000305475):n.459-8185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,176 control chromosomes in the GnomAD database, including 8,044 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 0.31 ( 8044 hom., cov: 32)

Consequence

ENSG00000305475
ENST00000811232.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.00

Publications

1 publications found

Variant links:

Genes affected

ENSG00000305475 (HGNC:):

ENSG00000305475 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000305475	ENST00000811232.1 link	n.459-8185T>C	intron_variant	Intron 1 of 1
ENSG00000305475	ENST00000811233.1 link	n.420-8185T>C	intron_variant	Intron 2 of 2
ENSG00000305475	ENST00000811234.1 link	n.161+4537T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46587

AN:

152058

Hom.:

8022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.406

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.297

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

GnomAD4 genome

AF:

0.307

AC:

46665

AN:

152176

Hom.:

8044

Cov.:

AF XY:

0.303

AC XY:

22546

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.459

AC:

19031

AN:

41494

American (AMR)

AF:

0.310

AC:

4734

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.406

AC:

1410

AN:

3470

East Asian (EAS)

AF:

0.114

AC:

591

AN:

5186

South Asian (SAS)

AF:

0.237

AC:

1145

AN:

4828

European-Finnish (FIN)

AF:

0.209

AC:

2212

AN:

10602

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.243

AC:

16552

AN:

67992

Other (OTH)

AF:

0.295

AC:

625

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1568

3136

4703

6271

7839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.278

Hom.:

2408

Bravo

AF:

0.318

Asia WGS

AF:

0.202

AC:

705

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.091

(source)

DANN

Benign

0.76

PhyloP100

-3.0

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