Genetic Variant ENSG00000298396:n.32+8436T>C (chr6-31279542-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755297.1(ENSG00000298396):n.32+8436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,172 control chromosomes in the GnomAD database, including 1,326 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 ( 1326 hom., cov: 32)

Consequence

ENSG00000298396
ENST00000755297.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.974

Publications

4 publications found

Variant links:

Genes affected

ENSG00000298396 (HGNC:):

ENSG00000298396 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=-0.63).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 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
ENSG00000298396	ENST00000755297.1 link	n.32+8436T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19190

AN:

152054

Hom.:

1326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.0670

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.0997

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.140

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

GnomAD4 genome

AF:

0.126

AC:

19198

AN:

152172

Hom.:

1326

Cov.:

AF XY:

0.127

AC XY:

9431

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.106

AC:

4404

AN:

41522

American (AMR)

AF:

0.110

AC:

1686

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1072

AN:

3468

East Asian (EAS)

AF:

0.0673

AC:

349

AN:

5184

South Asian (SAS)

AF:

0.179

AC:

862

AN:

4814

European-Finnish (FIN)

AF:

0.0997

AC:

1056

AN:

10588

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9204

AN:

67996

Other (OTH)

AF:

0.140

AC:

295

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

844

1688

2533

3377

4221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.127

Hom.:

188

Bravo

AF:

0.125

Asia WGS

AF:

0.133

AC:

463

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

0.97

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