Genetic Variant ENSG00000300178:n.*237A>G (chr20-31818295-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000769779.1(ENSG00000300178):n.*237A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 152,162 control chromosomes in the GnomAD database, including 660 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 0.088 ( 660 hom., cov: 32)

Consequence

ENSG00000300178
ENST00000769779.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.715

Publications

5 publications found

Variant links:

Genes affected

ENSG00000300178 (HGNC:):

ENSG00000300178 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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
ENSG00000300178	ENST00000769779.1 link	n.*237A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0875

AC:

13306

AN:

152044

Hom.:

657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.0621

Gnomad ASJ

AF:

0.0855

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0268

Gnomad FIN

AF:

0.0729

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.0963

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

GnomAD4 genome

AF:

0.0877

AC:

13340

AN:

152162

Hom.:

660

Cov.:

AF XY:

0.0849

AC XY:

6317

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.137

AC:

5671

AN:

41490

American (AMR)

AF:

0.0619

AC:

946

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0855

AC:

297

AN:

3472

East Asian (EAS)

AF:

0.000966

AC:

AN:

5178

South Asian (SAS)

AF:

0.0272

AC:

131

AN:

4816

European-Finnish (FIN)

AF:

0.0729

AC:

773

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0766

AC:

5208

AN:

68016

Other (OTH)

AF:

0.0957

AC:

202

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

613

1226

1839

2452

3065

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.0822

Hom.:

115

Bravo

AF:

0.0902

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.71

(source)

DANN

Benign

0.42

PhyloP100

-0.71

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