Genetic Variant ENSG00000300496:n.44+26764C>T (chr20-51209643-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000772384.1(ENSG00000300496):n.44+26764C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,172 control chromosomes in the GnomAD database, including 3,413 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 0.20 ( 3413 hom., cov: 32)

Consequence

ENSG00000300496
ENST00000772384.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.780

Publications

4 publications found

Variant links:

Genes affected

ENSG00000300496 (HGNC:):

ENSG00000300496 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=-0.48).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 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
ENSG00000300496	ENST00000772384.1 link	n.44+26764C>T		intron_variant	Intron 1 of 4
ENSG00000300496	ENST00000772385.1 link	n.80+26764C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30336

AN:

152054

Hom.:

3404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0962

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.0912

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.197

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

GnomAD4 genome

AF:

0.200

AC:

30373

AN:

152172

Hom.:

3413

Cov.:

AF XY:

0.202

AC XY:

15057

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0964

AC:

4003

AN:

41538

American (AMR)

AF:

0.269

AC:

4105

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

753

AN:

3468

East Asian (EAS)

AF:

0.177

AC:

917

AN:

5180

South Asian (SAS)

AF:

0.0922

AC:

444

AN:

4818

European-Finnish (FIN)

AF:

0.309

AC:

3272

AN:

10574

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16342

AN:

67990

Other (OTH)

AF:

0.197

AC:

416

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1248

2495

3743

4990

6238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.213

Hom.:

2659

Bravo

AF:

0.200

Asia WGS

AF:

0.162

AC:

564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.78

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