Genetic Variant ENSG00000303476:n.-96T>C (chr6-35436577-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 ENST00000794874.1(ENSG00000303476):n.-96T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,182 control chromosomes in the GnomAD database, including 32,572 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 0.63 ( 32572 hom., cov: 34)

Consequence

ENSG00000303476
ENST00000794874.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237

Publications

12 publications found

Variant links:

Genes affected

ENSG00000303476 (HGNC:):

ENSG00000303476 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000303476	ENST00000794874.1 link	n.-96T>C	upstream_gene_variant
ENSG00000303476	ENST00000794875.1 link	n.-113T>C	upstream_gene_variant
ENSG00000303476	ENST00000794876.1 link	n.-113T>C	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

96044

AN:

152066

Hom.:

32546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.660

Gnomad AMR

AF:

0.704

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.676

Gnomad FIN

AF:

0.814

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.754

Gnomad OTH

AF:

0.608

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

GnomAD4 genome

AF:

0.631

AC:

96097

AN:

152182

Hom.:

32572

Cov.:

AF XY:

0.633

AC XY:

47097

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.384

AC:

15948

AN:

41508

American (AMR)

AF:

0.704

AC:

10766

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.555

AC:

1925

AN:

3470

East Asian (EAS)

AF:

0.432

AC:

2234

AN:

5172

South Asian (SAS)

AF:

0.677

AC:

3271

AN:

4834

European-Finnish (FIN)

AF:

0.814

AC:

8634

AN:

10606

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.754

AC:

51254

AN:

67984

Other (OTH)

AF:

0.610

AC:

1288

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1681

3363

5044

6726

8407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.702

Hom.:

4872

Bravo

AF:

0.611

Asia WGS

AF:

0.524

AC:

1822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.45

(source)

DANN

Benign

0.40

PhyloP100

-0.24

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