Genetic Variant ENSG00000300530:n.42+12842A>G (chr1-162891123-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000772589.1(ENSG00000300530):n.42+12842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,102 control chromosomes in the GnomAD database, including 47,788 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 0.77 ( 47788 hom., cov: 31)

Consequence

ENSG00000300530
ENST00000772589.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

5 publications found

Variant links:

Genes affected

ENSG00000300530 (HGNC:):

ENSG00000300530 links:

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new If you want to explore the variant's impact on the transcript ENST00000772589.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772589.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300530	ENST00000772589.1		n.42+12842A>G		intron	N/A
	ENSG00000300530	ENST00000772590.1		n.80+12801A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117616

AN:

151984

Hom.:

47787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.894

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.734

Gnomad FIN

AF:

0.928

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.911

Gnomad OTH

AF:

0.799

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

GnomAD4 genome

AF:

0.774

AC:

117666

AN:

152102

Hom.:

47788

Cov.:

AF XY:

0.771

AC XY:

57296

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.549

AC:

22745

AN:

41442

American (AMR)

AF:

0.760

AC:

11602

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.894

AC:

3104

AN:

3472

East Asian (EAS)

AF:

0.425

AC:

2191

AN:

5158

South Asian (SAS)

AF:

0.734

AC:

3539

AN:

4824

European-Finnish (FIN)

AF:

0.928

AC:

9838

AN:

10598

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.911

AC:

61986

AN:

68014

Other (OTH)

AF:

0.798

AC:

1688

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1138

2276

3415

4553

5691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.872

Hom.:

101535

Bravo

AF:

0.750

Asia WGS

AF:

0.551

AC:

1913

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.95

(source)

DANN

Benign

0.41

PhyloP100

-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over