Genetic Variant ENSG00000300816:n.94-202G>A (chr4-25065843-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 ENST00000774230.1(ENSG00000300816):n.94-202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,220 control chromosomes in the GnomAD database, including 52,815 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 0.83 ( 52815 hom., cov: 32)

Consequence

ENSG00000300816
ENST00000774230.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

4 publications found

Variant links:

Genes affected

ENSG00000300816 (HGNC:):

ENSG00000300816 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300816	ENST00000774230.1 link	n.94-202G>A	intron_variant	Intron 1 of 3
ENSG00000300816	ENST00000774231.1 link	n.308-202G>A	intron_variant	Intron 1 of 2
ENSG00000300816	ENST00000774233.1 link	n.59-202G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.832

AC:

126617

AN:

152102

Hom.:

52763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.851

Gnomad AMR

AF:

0.840

Gnomad ASJ

AF:

0.830

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.846

Gnomad FIN

AF:

0.785

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.847

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

GnomAD4 genome

AF:

0.832

AC:

126723

AN:

152220

Hom.:

52815

Cov.:

AF XY:

0.830

AC XY:

61739

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.862

AC:

35820

AN:

41542

American (AMR)

AF:

0.840

AC:

12848

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.830

AC:

2881

AN:

3470

East Asian (EAS)

AF:

0.723

AC:

3739

AN:

5168

South Asian (SAS)

AF:

0.847

AC:

4088

AN:

4826

European-Finnish (FIN)

AF:

0.785

AC:

8308

AN:

10584

Middle Eastern (MID)

AF:

0.827

AC:

243

AN:

294

European-Non Finnish (NFE)

AF:

0.827

AC:

56235

AN:

68018

Other (OTH)

AF:

0.846

AC:

1787

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1088

2177

3265

4354

5442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<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:

0.835

Hom.:

100067

Bravo

AF:

0.837

Asia WGS

AF:

0.814

AC:

2830

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.28

(source)

DANN

Benign

0.60

PhyloP100

-1.4

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