Genetic Variant ENSG00000298809:n.129+1318C>G (chr6-110957720-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000758068.1(ENSG00000298809):n.129+1318C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 142,376 control chromosomes in the GnomAD database, including 1,734 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 0.14 ( 1734 hom., cov: 32)

Consequence

ENSG00000298809
ENST00000758068.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

0 publications found

Variant links:

Genes affected

ENSG00000298809 (HGNC:):

ENSG00000298809 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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
ENSG00000298809	ENST00000758068.1 link	n.129+1318C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

19876

AN:

142256

Hom.:

1727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.0889

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.0514

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.0592

Gnomad MID

AF:

0.176

Gnomad NFE

AF:

0.0944

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.140

AC:

19930

AN:

142376

Hom.:

1734

Cov.:

AF XY:

0.138

AC XY:

9566

AN XY:

69186

show subpopulations

African (AFR)

AF:

0.254

AC:

10334

AN:

40724

American (AMR)

AF:

0.0888

AC:

1296

AN:

14596

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

481

AN:

3420

East Asian (EAS)

AF:

0.0508

AC:

AN:

1888

South Asian (SAS)

AF:

0.152

AC:

660

AN:

4330

European-Finnish (FIN)

AF:

0.0592

AC:

561

AN:

9474

Middle Eastern (MID)

AF:

0.172

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0944

AC:

6131

AN:

64930

Other (OTH)

AF:

0.138

AC:

274

AN:

1986

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

869

1738

2606

3475

4344

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.0367

Hom.:

Bravo

AF:

0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.89

(source)

DANN

Benign

0.17

PhyloP100

-1.5

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