Genetic Variant ENSG00000305763:n.66+8239T>C (chr8-38474800-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 ENST00000812829.1(ENSG00000305763):n.66+8239T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,130 control chromosomes in the GnomAD database, including 10,592 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 0.37 ( 10592 hom., cov: 33)

Consequence

ENSG00000305763
ENST00000812829.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

Publications

36 publications found

Variant links:

Genes affected

ENSG00000305763 (HGNC:):

ENSG00000305763 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 (SAS) allele frequency at 95% confidence interval = 0.487 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
ENSG00000305763	ENST00000812829.1 link	n.66+8239T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55746

AN:

152012

Hom.:

10585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.279

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.503

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.343

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

GnomAD4 genome

AF:

0.367

AC:

55761

AN:

152130

Hom.:

10592

Cov.:

AF XY:

0.370

AC XY:

27501

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.279

AC:

11589

AN:

41518

American (AMR)

AF:

0.289

AC:

4420

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1209

AN:

3470

East Asian (EAS)

AF:

0.391

AC:

2021

AN:

5172

South Asian (SAS)

AF:

0.504

AC:

2426

AN:

4816

European-Finnish (FIN)

AF:

0.433

AC:

4577

AN:

10580

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.416

AC:

28281

AN:

67982

Other (OTH)

AF:

0.345

AC:

728

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1820

3640

5460

7280

9100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.394

Hom.:

54006

Bravo

AF:

0.347

Asia WGS

AF:

0.438

AC:

1521

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

6.2

(source)

DANN

Benign

0.80

PhyloP100

1.1

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