Genetic Variant ENSG00000303263:n.*88T>A (chr2-102245610-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000793262.1(ENSG00000303263):n.*88T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,870 control chromosomes in the GnomAD database, including 9,558 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 0.34 ( 9558 hom., cov: 31)

Consequence

ENSG00000303263
ENST00000793262.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.722

Publications

6 publications found

Variant links:

Genes affected

ENSG00000303263 (HGNC:):

ENSG00000303263 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000303263	ENST00000793262.1 link	n.*88T>A	downstream_gene_variant
ENSG00000303263	ENST00000793263.1 link	n.*89T>A	downstream_gene_variant
ENSG00000303263	ENST00000793264.1 link	n.*88T>A	downstream_gene_variant
ENSG00000303263	ENST00000793265.1 link	n.*27T>A	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51299

AN:

151752

Hom.:

9565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.376

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.330

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

GnomAD4 genome

AF:

0.338

AC:

51303

AN:

151870

Hom.:

9558

Cov.:

AF XY:

0.346

AC XY:

25643

AN XY:

74204

show subpopulations

African (AFR)

AF:

0.218

AC:

9035

AN:

41410

American (AMR)

AF:

0.294

AC:

4496

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

840

AN:

3472

East Asian (EAS)

AF:

0.671

AC:

3460

AN:

5154

South Asian (SAS)

AF:

0.595

AC:

2856

AN:

4802

European-Finnish (FIN)

AF:

0.418

AC:

4400

AN:

10538

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.369

AC:

25081

AN:

67918

Other (OTH)

AF:

0.335

AC:

705

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

1561

3122

4684

6245

7806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.233

Hom.:

588

Bravo

AF:

0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.63

(source)

DANN

Benign

0.55

PhyloP100

-0.72

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