Genetic Variant ENSG00000301543:n.118-230T>C (chr7-16065520-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000779607.1(ENSG00000301543):n.118-230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,154 control chromosomes in the GnomAD database, including 728 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 0.077 ( 728 hom., cov: 32)

Consequence

ENSG00000301543
ENST00000779607.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.788

Publications

2 publications found

Variant links:

Genes affected

ENSG00000301543 (HGNC:):

ENSG00000301543 links:

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new If you want to explore the variant's impact on the transcript ENST00000779607.1, 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779607.1. 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
	ENSG00000301543	ENST00000779607.1		n.118-230T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0773

AC:

11759

AN:

152036

Hom.:

723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0578

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0226

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.0891

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

GnomAD4 genome

AF:

0.0775

AC:

11791

AN:

152154

Hom.:

728

Cov.:

AF XY:

0.0774

AC XY:

5760

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.121

AC:

5027

AN:

41532

American (AMR)

AF:

0.0577

AC:

881

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

629

AN:

3470

East Asian (EAS)

AF:

0.309

AC:

1589

AN:

5150

South Asian (SAS)

AF:

0.0751

AC:

362

AN:

4822

European-Finnish (FIN)

AF:

0.0226

AC:

240

AN:

10614

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0416

AC:

2825

AN:

67982

Other (OTH)

AF:

0.0900

AC:

190

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

532

1065

1597

2130

2662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

134

268

402

536

670

<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:

0.0157

Hom.:

Bravo

AF:

0.0844

Asia WGS

AF:

0.178

AC:

618

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.27

(source)

DANN

Benign

0.57

PhyloP100

-0.79

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