Genetic Variant ENST00000756734.1:n.96+55346A>G (chr18-71487494-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000756734.1(ENSG00000298599):n.96+55346A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 151,784 control chromosomes in the GnomAD database, including 319 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 0.054 ( 319 hom., cov: 31)

Consequence

ENSG00000298599
ENST00000756734.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330

Publications

3 publications found

Variant links:

Genes affected

ENSG00000298599 (HGNC:):

ENSG00000298599 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985179	XR_001753502.1 link	n.64+55346A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298599	ENST00000756734.1 link	n.96+55346A>G	intron_variant	Intron 1 of 4
ENSG00000298599	ENST00000756735.1 link	n.52+55346A>G	intron_variant	Intron 1 of 2
ENSG00000298599	ENST00000756736.1 link	n.134+55346A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0538

AC:

8165

AN:

151664

Hom.:

320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0106

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.0261

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.0226

Gnomad NFE

AF:

0.0668

Gnomad OTH

AF:

0.0467

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

GnomAD4 genome

AF:

0.0538

AC:

8170

AN:

151784

Hom.:

319

Cov.:

AF XY:

0.0567

AC XY:

4206

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.0106

AC:

439

AN:

41514

American (AMR)

AF:

0.0261

AC:

396

AN:

15176

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

211

AN:

3472

East Asian (EAS)

AF:

0.125

AC:

645

AN:

5146

South Asian (SAS)

AF:

0.146

AC:

703

AN:

4810

European-Finnish (FIN)

AF:

0.102

AC:

1077

AN:

10524

Middle Eastern (MID)

AF:

0.0208

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0668

AC:

4534

AN:

67844

Other (OTH)

AF:

0.0481

AC:

101

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

373

746

1120

1493

1866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0595

Hom.:

547

Bravo

AF:

0.0429

Asia WGS

AF:

0.122

AC:

425

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.3

(source)

DANN

Benign

0.58

PhyloP100

-0.033

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