Genetic Variant ENST00000799383.1:n.958-20472C>T (chr2-155780197-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 ENST00000799383.1(ENSG00000304068):n.958-20472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 151,650 control chromosomes in the GnomAD database, including 3,156 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 0.18 ( 3156 hom., cov: 32)

Consequence

ENSG00000304068
ENST00000799383.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

1 publications found

Variant links:

Genes affected

ENSG00000304068 (HGNC:):

ENSG00000304068 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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373703	XR_007088689.1 link	n.896-20472C>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304068	ENST00000799383.1 link	n.958-20472C>T		intron_variant	Intron 7 of 8
ENSG00000304068	ENST00000799386.1 link	n.83-20472C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27636

AN:

151530

Hom.:

3159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0594

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.0473

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.298

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.182

AC:

27629

AN:

151650

Hom.:

3156

Cov.:

AF XY:

0.177

AC XY:

13129

AN XY:

74130

show subpopulations

African (AFR)

AF:

0.0593

AC:

2457

AN:

41464

American (AMR)

AF:

0.160

AC:

2432

AN:

15158

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

944

AN:

3462

East Asian (EAS)

AF:

0.0470

AC:

242

AN:

5144

South Asian (SAS)

AF:

0.119

AC:

573

AN:

4816

European-Finnish (FIN)

AF:

0.210

AC:

2221

AN:

10564

Middle Eastern (MID)

AF:

0.284

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.264

AC:

17893

AN:

67730

Other (OTH)

AF:

0.196

AC:

414

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1083

2166

3250

4333

5416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.237

Hom.:

3450

Bravo

AF:

0.173

Asia WGS

AF:

0.0940

AC:

329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.10

(source)

DANN

Benign

0.41

PhyloP100

-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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