Genetic Variant ENSG00000308660:n.290+332C>T (chr5-71922769-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000835588.1(ENSG00000308660):n.290+332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,992 control chromosomes in the GnomAD database, including 2,282 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 0.13 ( 2282 hom., cov: 32)

Consequence

ENSG00000308660
ENST00000835588.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.267

Publications

6 publications found

Variant links:

Genes affected

ENSG00000308660 (HGNC:):

ENSG00000308660 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 (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986382	XR_001742515.2 link	n.213+332C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000308660	ENST00000835588.1 link	n.290+332C>T	intron_variant	Intron 2 of 2
ENSG00000308660	ENST00000835589.1 link	n.-92C>T	upstream_gene_variant
ENSG00000308660	ENST00000835590.1 link	n.-82C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19337

AN:

151874

Hom.:

2266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.0745

Gnomad ASJ

AF:

0.0931

Gnomad EAS

AF:

0.0671

Gnomad SAS

AF:

0.0388

Gnomad FIN

AF:

0.0333

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0539

Gnomad OTH

AF:

0.104

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

GnomAD4 genome

AF:

0.128

AC:

19385

AN:

151992

Hom.:

2282

Cov.:

AF XY:

0.124

AC XY:

9209

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.312

AC:

12932

AN:

41416

American (AMR)

AF:

0.0744

AC:

1136

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0931

AC:

323

AN:

3470

East Asian (EAS)

AF:

0.0666

AC:

344

AN:

5162

South Asian (SAS)

AF:

0.0389

AC:

187

AN:

4812

European-Finnish (FIN)

AF:

0.0333

AC:

352

AN:

10572

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0539

AC:

3667

AN:

67980

Other (OTH)

AF:

0.103

AC:

218

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

751

1501

2252

3002

3753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.0641

Hom.:

259

Bravo

AF:

0.139

Asia WGS

AF:

0.0700

AC:

246

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.5

(source)

DANN

Benign

0.59

PhyloP100

0.27

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