Genetic Variant ENSG00000286288:n.92-50A>C (chr20-1811274-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 ENST00000447206.2(ENSG00000286288):n.92-50A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,924 control chromosomes in the GnomAD database, including 25,072 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 0.57 ( 25057 hom., cov: 30)

Exomes 𝑓: 0.62 ( 15 hom. )

Consequence

ENSG00000286288
ENST00000447206.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.202

Publications

10 publications found

Variant links:

Genes affected

ENSG00000286288 (HGNC:):

ENSG00000286288 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 (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000286288	ENST00000447206.2 link	n.92-50A>C	intron_variant	Intron 1 of 5	2
ENSG00000286288	ENST00000654380.1 link	n.81-600A>C	intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000658107.1 link	n.92-600A>C	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86119

AN:

151732

Hom.:

25038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.672

Gnomad NFE

AF:

0.616

Gnomad OTH

AF:

0.601

GnomAD4 exome

AF:

0.622

AC:

AN:

Hom.:

Cov.:

AF XY:

0.640

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.672

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.567

AC:

86172

AN:

151850

Hom.:

25057

Cov.:

AF XY:

0.566

AC XY:

41978

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.442

AC:

18291

AN:

41414

American (AMR)

AF:

0.655

AC:

9994

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.654

AC:

2268

AN:

3466

East Asian (EAS)

AF:

0.724

AC:

3731

AN:

5156

South Asian (SAS)

AF:

0.593

AC:

2856

AN:

4816

European-Finnish (FIN)

AF:

0.509

AC:

5377

AN:

10560

Middle Eastern (MID)

AF:

0.668

AC:

195

AN:

292

European-Non Finnish (NFE)

AF:

0.616

AC:

41790

AN:

67868

Other (OTH)

AF:

0.602

AC:

1270

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1850

3700

5551

7401

9251

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.610

Hom.:

40491

Bravo

AF:

0.575

Asia WGS

AF:

0.588

AC:

2045

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

6.4

(source)

DANN

Benign

0.79

PhyloP100

-0.20

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over