Genetic Variant ENST00000715178.1:n.1038-21087C>G (chr6-78225040-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 ENST00000715178.1(ENSG00000230309):n.1038-21087C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 150,552 control chromosomes in the GnomAD database, including 4,180 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 0.22 ( 4180 hom., cov: 31)

Consequence

ENSG00000230309
ENST00000715178.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

Publications

4 publications found

Variant links:

Genes affected

ENSG00000230309 (HGNC:):

ENSG00000230309 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2 link	n.135-21087C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1 link	n.1038-21087C>G		intron_variant	Intron 6 of 14

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32549

AN:

150454

Hom.:

4178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.100

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.210

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

GnomAD4 genome

AF:

0.216

AC:

32571

AN:

150552

Hom.:

4180

Cov.:

AF XY:

0.221

AC XY:

16239

AN XY:

73504

show subpopulations

African (AFR)

AF:

0.299

AC:

12174

AN:

40744

American (AMR)

AF:

0.297

AC:

4505

AN:

15160

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

810

AN:

3442

East Asian (EAS)

AF:

0.495

AC:

2498

AN:

5048

South Asian (SAS)

AF:

0.180

AC:

862

AN:

4802

European-Finnish (FIN)

AF:

0.165

AC:

1732

AN:

10480

Middle Eastern (MID)

AF:

0.0972

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.138

AC:

9338

AN:

67592

Other (OTH)

AF:

0.210

AC:

438

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1222

2444

3666

4888

6110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0741

Hom.:

Bravo

AF:

0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.44

(source)

DANN

Benign

0.64

PhyloP100

0.013

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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ENST00000715178.1:n.1038-21087C>G

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