Genetic Variant ENSG00000297913:n.108-11181A>G (chr1-159715346-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000751816.1(ENSG00000297913):n.108-11181A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,622 control chromosomes in the GnomAD database, including 1,826 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 0.13 ( 1826 hom., cov: 30)

Consequence

ENSG00000297913
ENST00000751816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240

Publications

112 publications found

Variant links:

Genes affected

ENSG00000297913 (HGNC:):

ENSG00000297913 links:

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new If you want to explore the variant's impact on the transcript ENST00000751816.1, 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000297913	ENST00000751816.1	n.108-11181A>G	intron	N/A
ENSG00000297913	ENST00000751817.1	n.110-11181A>G	intron	N/A
ENSG00000297913	ENST00000751818.1	n.63-11181A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18934

AN:

151504

Hom.:

1818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.0748

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0648

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.0614

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.125

AC:

18967

AN:

151622

Hom.:

1826

Cov.:

AF XY:

0.124

AC XY:

9202

AN XY:

74140

show subpopulations

African (AFR)

AF:

0.265

AC:

10950

AN:

41262

American (AMR)

AF:

0.0747

AC:

1138

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

406

AN:

3466

East Asian (EAS)

AF:

0.153

AC:

786

AN:

5146

South Asian (SAS)

AF:

0.102

AC:

490

AN:

4790

European-Finnish (FIN)

AF:

0.0648

AC:

680

AN:

10500

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0613

AC:

4165

AN:

67920

Other (OTH)

AF:

0.123

AC:

259

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

732

1464

2196

2928

3660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.0808

Hom.:

3288

Bravo

AF:

0.131

Asia WGS

AF:

0.107

AC:

370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

(source)

DANN

Benign

0.57

PhyloP100

-0.024

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