Genetic Variant ENST00000504861.3:n.58+12390A>C (chr8-92865193-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000504861.3(FLJ46284):n.58+12390A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 152,094 control chromosomes in the GnomAD database, including 454 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 0.049 ( 454 hom., cov: 32)

Consequence

FLJ46284
ENST00000504861.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found

Variant links:

Genes affected

FLJ46284 (HGNC:):

FLJ46284 links:

ENSG00000253577 (HGNC:58428):

ENSG00000253577 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 (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901978	XR_007061007.1 link	n.9468+173A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FLJ46284	ENST00000504861.3 link	n.58+12390A>C	intron_variant	Intron 1 of 3	2
FLJ46284	ENST00000744035.1 link	n.69+12354A>C	intron_variant	Intron 1 of 2
FLJ46284	ENST00000744036.1 link	n.91+12354A>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0493

AC:

7490

AN:

151976

Hom.:

452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0228

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.0417

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.0288

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00938

Gnomad OTH

AF:

0.0340

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

GnomAD4 genome

AF:

0.0494

AC:

7507

AN:

152094

Hom.:

454

Cov.:

AF XY:

0.0500

AC XY:

3719

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.140

AC:

5820

AN:

41464

American (AMR)

AF:

0.0227

AC:

346

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0110

AC:

AN:

3470

East Asian (EAS)

AF:

0.0416

AC:

215

AN:

5164

South Asian (SAS)

AF:

0.0108

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0288

AC:

305

AN:

10606

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00937

AC:

637

AN:

67974

Other (OTH)

AF:

0.0336

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

341

683

1024

1366

1707

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0358

Hom.:

Bravo

AF:

0.0529

Asia WGS

AF:

0.0290

AC:

102

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

0.56

(source)

DANN

Benign

0.55

PhyloP100

-1.0

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