Genetic Variant ENSG00000309192:n.53+4707C>T (chr2-145294184-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000839437.1(ENSG00000309192):n.53+4707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,580 control chromosomes in the GnomAD database, including 2,180 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 0.16 ( 2180 hom., cov: 31)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

ENSG00000309192
ENST00000839437.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

0 publications found

Variant links:

Genes affected

ENSG00000309192 (HGNC:):

ENSG00000309192 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309192	ENST00000839437.1 link	n.53+4707C>T	intron_variant	Intron 1 of 2
ENSG00000309192	ENST00000839438.1 link	n.53+4707C>T	intron_variant	Intron 1 of 2
ENSG00000309192	ENST00000839439.1 link	n.53+4707C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23535

AN:

151456

Hom.:

2176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0694

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.173

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.155

AC:

23565

AN:

151574

Hom.:

2180

Cov.:

AF XY:

0.156

AC XY:

11545

AN XY:

74058

show subpopulations

African (AFR)

AF:

0.187

AC:

7753

AN:

41362

American (AMR)

AF:

0.250

AC:

3795

AN:

15184

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

497

AN:

3464

East Asian (EAS)

AF:

0.374

AC:

1909

AN:

5106

South Asian (SAS)

AF:

0.161

AC:

776

AN:

4808

European-Finnish (FIN)

AF:

0.0694

AC:

729

AN:

10504

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7571

AN:

67840

Other (OTH)

AF:

0.171

AC:

359

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

979

1958

2936

3915

4894

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.0611

Hom.:

Bravo

AF:

0.175

Asia WGS

AF:

0.248

AC:

862

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

(source)

DANN

Benign

0.32

PhyloP100

-1.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over