Genetic Variant ENSG00000287290:n.213-1243A>C (chr4-116954105-T-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000824997.1(ENSG00000287290):n.213-1243A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,898 control chromosomes in the GnomAD database, including 3,870 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 0.22 ( 3870 hom., cov: 32)

Consequence

ENSG00000287290
ENST00000824997.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0900

Publications

6 publications found

Variant links:

Genes affected

ENSG00000287290 (HGNC:):

ENSG00000287290 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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
ENSG00000287290	ENST00000824997.1 link	n.213-1243A>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33843

AN:

151778

Hom.:

3868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.223

AC:

33861

AN:

151898

Hom.:

3870

Cov.:

AF XY:

0.223

AC XY:

16525

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.208

AC:

8635

AN:

41488

American (AMR)

AF:

0.250

AC:

3810

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.290

AC:

1005

AN:

3464

East Asian (EAS)

AF:

0.281

AC:

1436

AN:

5110

South Asian (SAS)

AF:

0.270

AC:

1302

AN:

4822

European-Finnish (FIN)

AF:

0.157

AC:

1660

AN:

10606

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.222

AC:

15034

AN:

67856

Other (OTH)

AF:

0.261

AC:

550

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1352

2705

4057

5410

6762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.208

Hom.:

2060

Bravo

AF:

0.226

Asia WGS

AF:

0.270

AC:

939

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

0.090

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