Genetic Variant ENST00000596881.2:n.254-292G>C (chr19-53303399-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000596881.2(ENSG00000290987):n.254-292G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.24 ( 308 hom., cov: 0)

Consequence

ENSG00000290987
ENST00000596881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.885

Publications

1 publications found

Variant links:

Genes affected

ENSG00000290987 (HGNC:):

ENSG00000290987 links:

FAM90A28P (HGNC:43747): (family with sequence similarity 90 member A28, pseudogene)

FAM90A28P 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987270	XR_001753995.1 link	n.188-292G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290987	ENST00000596881.2 link	n.254-292G>C		intron_variant	Intron 2 of 6	5
FAM90A28P	ENST00000597191.2 link	n.73-292G>C		intron_variant	Intron 1 of 5	6

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

8103

AN:

33772

Hom.:

307

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.0930

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.262

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

GnomAD4 genome

AF:

0.240

AC:

8114

AN:

33818

Hom.:

308

Cov.:

AF XY:

0.237

AC XY:

3881

AN XY:

16398

show subpopulations

African (AFR)

AF:

0.343

AC:

4009

AN:

11684

American (AMR)

AF:

0.163

AC:

613

AN:

3770

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

143

AN:

604

East Asian (EAS)

AF:

0.264

AC:

325

AN:

1232

South Asian (SAS)

AF:

0.195

AC:

190

AN:

974

European-Finnish (FIN)

AF:

0.164

AC:

329

AN:

2006

Middle Eastern (MID)

AF:

0.186

AC:

AN:

European-Non Finnish (NFE)

AF:

0.183

AC:

2365

AN:

12938

Other (OTH)

AF:

0.262

AC:

119

AN:

454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

381

762

1142

1523

1904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.133

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.44

(source)

DANN

Benign

0.21

PhyloP100

-0.89

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