dbSNP rs939898: ENSG00000297389:n.66-2312A>G (chr12-91273693-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 ENST00000747678.1(ENSG00000297389):n.66-2312A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,204 control chromosomes in the GnomAD database, including 1,658 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 0.13 ( 1658 hom., cov: 32)

Consequence

ENSG00000297389
ENST00000747678.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549

Publications

6 publications found

Variant links:

Genes affected

ENSG00000297389 (HGNC:):

ENSG00000297389 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297389	ENST00000747678.1 link	n.66-2312A>G	intron_variant	Intron 1 of 4
ENSG00000297389	ENST00000747679.1 link	n.66-16553A>G	intron_variant	Intron 1 of 3
ENSG00000297389	ENST00000747680.1 link	n.70-2312A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20266

AN:

152086

Hom.:

1659

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0607

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00462

Gnomad SAS

AF:

0.0624

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.133

AC:

20265

AN:

152204

Hom.:

1658

Cov.:

AF XY:

0.130

AC XY:

9678

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0605

AC:

2515

AN:

41542

American (AMR)

AF:

0.145

AC:

2220

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

533

AN:

3468

East Asian (EAS)

AF:

0.00463

AC:

AN:

5178

South Asian (SAS)

AF:

0.0620

AC:

299

AN:

4822

European-Finnish (FIN)

AF:

0.128

AC:

1357

AN:

10594

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.188

AC:

12783

AN:

68000

Other (OTH)

AF:

0.162

AC:

342

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

853

1706

2558

3411

4264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.154

Hom.:

336

Bravo

AF:

0.133

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.89

(source)

DANN

Benign

0.44

PhyloP100

-0.55

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