Genetic Variant ENSG00000308664:n.427-12321G>C (chr12-16095189-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000835597.1(ENSG00000308664):n.427-12321G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,192 control chromosomes in the GnomAD database, including 813 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 0.069 ( 813 hom., cov: 33)

Consequence

ENSG00000308664
ENST00000835597.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

0 publications found

Variant links:

Genes affected

ENSG00000308664 (HGNC:):

ENSG00000308664 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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
ENSG00000308664	ENST00000835597.1 link	n.427-12321G>C		intron_variant	Intron 1 of 1
ENSG00000308664	ENST00000835598.1 link	n.355-12321G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0694

AC:

10548

AN:

152074

Hom.:

814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0510

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0374

Gnomad ASJ

AF:

0.0556

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0455

Gnomad OTH

AF:

0.0568

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

GnomAD4 genome

AF:

0.0693

AC:

10554

AN:

152192

Hom.:

813

Cov.:

AF XY:

0.0774

AC XY:

5759

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0510

AC:

2117

AN:

41512

American (AMR)

AF:

0.0374

AC:

572

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0556

AC:

193

AN:

3472

East Asian (EAS)

AF:

0.423

AC:

2185

AN:

5170

South Asian (SAS)

AF:

0.183

AC:

881

AN:

4812

European-Finnish (FIN)

AF:

0.129

AC:

1369

AN:

10590

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0455

AC:

3094

AN:

68008

Other (OTH)

AF:

0.0581

AC:

123

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

465

930

1395

1860

2325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0273

Hom.:

Bravo

AF:

0.0619

Asia WGS

AF:

0.272

AC:

944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.1

(source)

DANN

Benign

0.53

PhyloP100

0.16

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