dbSNP rs2658161: ENSG00000308020:n.214-39774T>C (chr5-8133581-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 ENST00000830491.1(ENSG00000308020):n.214-39774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,038 control chromosomes in the GnomAD database, including 273 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 0.056 ( 273 hom., cov: 32)

Consequence

ENSG00000308020
ENST00000830491.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.445

Publications

1 publications found

Variant links:

Genes affected

ENSG00000308020 (HGNC:):

ENSG00000308020 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0605 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
ENSG00000308020	ENST00000830491.1 link	n.214-39774T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0558

AC:

8477

AN:

151922

Hom.:

274

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0588

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.0535

Gnomad ASJ

AF:

0.0484

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0232

Gnomad FIN

AF:

0.0439

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0621

Gnomad OTH

AF:

0.0560

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

GnomAD4 genome

AF:

0.0558

AC:

8485

AN:

152038

Hom.:

273

Cov.:

AF XY:

0.0537

AC XY:

3991

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.0588

AC:

2444

AN:

41534

American (AMR)

AF:

0.0534

AC:

814

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.0484

AC:

168

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0230

AC:

111

AN:

4830

European-Finnish (FIN)

AF:

0.0439

AC:

462

AN:

10522

Middle Eastern (MID)

AF:

0.0822

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0621

AC:

4218

AN:

67946

Other (OTH)

AF:

0.0555

AC:

117

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

398

796

1193

1591

1989

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0640

Hom.:

473

Bravo

AF:

0.0583

Asia WGS

AF:

0.0170

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.0

(source)

DANN

Benign

0.67

PhyloP100

0.45

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