Genetic Variant ENSG00000310078:n.865-183T>C (chr1-67639770-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 ENST00000846983.1(ENSG00000310078):n.865-183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,168 control chromosomes in the GnomAD database, including 3,697 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 0.17 ( 3697 hom., cov: 32)

Consequence

ENSG00000310078
ENST00000846983.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.675

Publications

3 publications found

Variant links:

Genes affected

ENSG00000310078 (HGNC:):

ENSG00000310078 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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
ENSG00000310078	ENST00000846983.1 link	n.865-183T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25314

AN:

152050

Hom.:

3672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.0529

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.167

AC:

25389

AN:

152168

Hom.:

3697

Cov.:

AF XY:

0.171

AC XY:

12735

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.379

AC:

15707

AN:

41486

American (AMR)

AF:

0.125

AC:

1909

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

AN:

3470

East Asian (EAS)

AF:

0.320

AC:

1657

AN:

5172

South Asian (SAS)

AF:

0.187

AC:

900

AN:

4820

European-Finnish (FIN)

AF:

0.116

AC:

1227

AN:

10596

Middle Eastern (MID)

AF:

0.0411

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0530

AC:

3602

AN:

68002

Other (OTH)

AF:

0.143

AC:

302

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

928

1855

2783

3710

4638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

258

516

774

1032

1290

<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:

0.112

Hom.:

3203

Bravo

AF:

0.174

Asia WGS

AF:

0.268

AC:

931

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.0020

(source)

DANN

Benign

0.44

PhyloP100

-0.68

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