dbSNP rs983152: ENSG00000302597:n.315+14977A>C (chr7-145113079-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000788025.1(ENSG00000302597):n.315+14977A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,064 control chromosomes in the GnomAD database, including 6,764 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 0.30 ( 6764 hom., cov: 32)

Consequence

ENSG00000302597
ENST00000788025.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.53

Publications

0 publications found

Variant links:

Genes affected

ENSG00000302597 (HGNC:):

ENSG00000302597 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 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
ENSG00000302597	ENST00000788025.1 link	n.315+14977A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44886

AN:

151946

Hom.:

6765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.337

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

GnomAD4 genome

AF:

0.295

AC:

44892

AN:

152064

Hom.:

6764

Cov.:

AF XY:

0.291

AC XY:

21601

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.263

AC:

10903

AN:

41488

American (AMR)

AF:

0.276

AC:

4211

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.389

AC:

1349

AN:

3468

East Asian (EAS)

AF:

0.210

AC:

1082

AN:

5164

South Asian (SAS)

AF:

0.245

AC:

1181

AN:

4828

European-Finnish (FIN)

AF:

0.243

AC:

2569

AN:

10574

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.330

AC:

22426

AN:

67958

Other (OTH)

AF:

0.335

AC:

709

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1636

3273

4909

6546

8182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.319

Hom.:

1675

Bravo

AF:

0.297

Asia WGS

AF:

0.218

AC:

759

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.12

(source)

DANN

Benign

0.54

PhyloP100

-2.5

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