Genetic Variant ENST00000798472.1:n.376+512A>G (chr5-148825809-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000798472.1(ENSG00000303969):n.376+512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,046 control chromosomes in the GnomAD database, including 27,782 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 0.60 ( 27775 hom., cov: 32)

Exomes 𝑓: 0.59 ( 7 hom. )

Consequence

ENSG00000303969
ENST00000798472.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.863

Publications

34 publications found

Variant links:

Genes affected

ENSG00000303969 (HGNC:):

ENSG00000303969 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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
ENSG00000303969	ENST00000798472.1 link	n.376+512A>G		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1 link	n.349+512A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91077

AN:

151896

Hom.:

27756

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.559

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.748

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.627

GnomAD4 exome

AF:

0.594

AC:

AN:

Hom.:

Cov.:

AF XY:

0.654

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.585

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.600

AC:

91141

AN:

152014

Hom.:

27775

Cov.:

AF XY:

0.607

AC XY:

45098

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.564

AC:

23378

AN:

41432

American (AMR)

AF:

0.713

AC:

10904

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.615

AC:

2134

AN:

3468

East Asian (EAS)

AF:

0.747

AC:

3842

AN:

5142

South Asian (SAS)

AF:

0.744

AC:

3582

AN:

4816

European-Finnish (FIN)

AF:

0.632

AC:

6690

AN:

10578

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.567

AC:

38549

AN:

67966

Other (OTH)

AF:

0.633

AC:

1336

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1825

3651

5476

7302

9127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

758

1516

2274

3032

3790

<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:

0.579

Hom.:

46094

Bravo

AF:

0.601

Asia WGS

AF:

0.754

AC:

2618

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.8

(source)

DANN

Benign

0.67

PhyloP100

-0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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