Genetic Variant ENSG00000300834:n.210-4609C>T (chr20-39552181-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 ENST00000774323.1(ENSG00000300834):n.210-4609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,228 control chromosomes in the GnomAD database, including 207 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 0.043 ( 207 hom., cov: 32)

Consequence

ENSG00000300834
ENST00000774323.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.906

Publications

0 publications found

Variant links:

Genes affected

ENSG00000300834 (HGNC:):

ENSG00000300834 links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0821 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
ENSG00000300834	ENST00000774323.1 link	n.210-4609C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0427

AC:

6499

AN:

152110

Hom.:

205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0857

Gnomad ASJ

AF:

0.0291

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0387

Gnomad FIN

AF:

0.0316

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0589

Gnomad OTH

AF:

0.0302

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

GnomAD4 genome

AF:

0.0428

AC:

6508

AN:

152228

Hom.:

207

Cov.:

AF XY:

0.0424

AC XY:

3154

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0110

AC:

456

AN:

41552

American (AMR)

AF:

0.0860

AC:

1316

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0291

AC:

101

AN:

3470

East Asian (EAS)

AF:

0.000194

AC:

AN:

5152

South Asian (SAS)

AF:

0.0394

AC:

190

AN:

4824

European-Finnish (FIN)

AF:

0.0316

AC:

335

AN:

10604

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0589

AC:

4006

AN:

68010

Other (OTH)

AF:

0.0299

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

318

636

955

1273

1591

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0180

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

0.91

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