Genetic Variant ENST00000782117.1:n.217+19018C>T (chr5-71950137-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000782117.1(ENSG00000301834):n.217+19018C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,150 control chromosomes in the GnomAD database, including 2,718 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 0.18 ( 2718 hom., cov: 32)

Consequence

ENSG00000301834
ENST00000782117.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301834 (HGNC:):

ENSG00000301834 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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
ENSG00000301834	ENST00000782117.1 link	n.217+19018C>T		intron_variant	Intron 1 of 2
ENSG00000301834	ENST00000782118.1 link	n.216+19018C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27846

AN:

152032

Hom.:

2714

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.187

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

GnomAD4 genome

AF:

0.183

AC:

27876

AN:

152150

Hom.:

2718

Cov.:

AF XY:

0.187

AC XY:

13901

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.174

AC:

7233

AN:

41512

American (AMR)

AF:

0.244

AC:

3730

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

473

AN:

3468

East Asian (EAS)

AF:

0.351

AC:

1816

AN:

5172

South Asian (SAS)

AF:

0.279

AC:

1343

AN:

4820

European-Finnish (FIN)

AF:

0.190

AC:

2010

AN:

10588

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10713

AN:

68004

Other (OTH)

AF:

0.190

AC:

401

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1149

2298

3448

4597

5746

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.164

Hom.:

3273

Bravo

AF:

0.187

Asia WGS

AF:

0.328

AC:

1139

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.5

(source)

DANN

Benign

0.39

PhyloP100

-0.35

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