dbSNP rs56403768: ENSG00000301363:n.617+15145A>G (chr6-118382371-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 ENST00000778490.1(ENSG00000301363):n.617+15145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,088 control chromosomes in the GnomAD database, including 9,399 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 0.34 ( 9399 hom., cov: 32)

Consequence

ENSG00000301363
ENST00000778490.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.174

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301363 (HGNC:):

ENSG00000301363 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301363	ENST00000778490.1 link	n.617+15145A>G	intron_variant	Intron 1 of 1
ENSG00000301363	ENST00000778491.1 link	n.158+15145A>G	intron_variant	Intron 1 of 3
ENSG00000301363	ENST00000778492.1 link	n.621+15145A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51255

AN:

151972

Hom.:

9401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.303

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

GnomAD4 genome

AF:

0.337

AC:

51275

AN:

152088

Hom.:

9399

Cov.:

AF XY:

0.333

AC XY:

24772

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.219

AC:

9076

AN:

41504

American (AMR)

AF:

0.237

AC:

3617

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

1138

AN:

3466

East Asian (EAS)

AF:

0.250

AC:

1293

AN:

5166

South Asian (SAS)

AF:

0.346

AC:

1669

AN:

4824

European-Finnish (FIN)

AF:

0.431

AC:

4552

AN:

10562

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.424

AC:

28853

AN:

67972

Other (OTH)

AF:

0.303

AC:

640

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1692

3383

5075

6766

8458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.315

Hom.:

1797

Bravo

AF:

0.317

Asia WGS

AF:

0.281

AC:

975

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.6

(source)

DANN

Benign

0.54

PhyloP100

0.17

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