Genetic Variant ENSG00000306370:n.28-8405A>G (chr8-36990191-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000817282.1(ENSG00000306370):n.28-8405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,084 control chromosomes in the GnomAD database, including 5,671 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 0.25 ( 5671 hom., cov: 32)

Consequence

ENSG00000306370
ENST00000817282.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14

Publications

10 publications found

Variant links:

Genes affected

ENSG00000306370 (HGNC:):

ENSG00000306370 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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
ENSG00000306370	ENST00000817282.1 link	n.28-8405A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38657

AN:

151966

Hom.:

5669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.391

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.254

AC:

38674

AN:

152084

Hom.:

5671

Cov.:

AF XY:

0.254

AC XY:

18916

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.390

AC:

16184

AN:

41476

American (AMR)

AF:

0.230

AC:

3512

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

983

AN:

3472

East Asian (EAS)

AF:

0.331

AC:

1713

AN:

5170

South Asian (SAS)

AF:

0.302

AC:

1451

AN:

4812

European-Finnish (FIN)

AF:

0.136

AC:

1439

AN:

10606

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12483

AN:

67974

Other (OTH)

AF:

0.250

AC:

527

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1400

2799

4199

5598

6998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.211

Hom.:

10740

Bravo

AF:

0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.6

(source)

DANN

Benign

0.74

PhyloP100

1.1

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