Genetic Variant ENSG00000230647:n.164G>C (chr17-14463621-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 ENST00000700765.2(ENSG00000230647):n.164G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,160 control chromosomes in the GnomAD database, including 2,493 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 0.11 ( 2493 hom., cov: 33)

Consequence

ENSG00000230647
ENST00000700765.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108

Publications

1 publications found

Variant links:

Genes affected

ENSG00000230647 (HGNC:58488):

ENSG00000230647 links:

Genome browser will be placed here

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 = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000230647	ENST00000700765.2 link	n.164G>C	non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000230647	ENST00000822015.1 link	n.239G>C	non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000230647	ENST00000822016.1 link	n.300G>C	non_coding_transcript_exon_variant	Exon 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17169

AN:

152042

Hom.:

2476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0562

Gnomad ASJ

AF:

0.0332

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0935

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0856

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

GnomAD4 genome

AF:

0.113

AC:

17248

AN:

152160

Hom.:

2493

Cov.:

AF XY:

0.112

AC XY:

8366

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.336

AC:

13928

AN:

41450

American (AMR)

AF:

0.0565

AC:

865

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0332

AC:

115

AN:

3468

East Asian (EAS)

AF:

0.187

AC:

965

AN:

5154

South Asian (SAS)

AF:

0.0930

AC:

449

AN:

4830

European-Finnish (FIN)

AF:

0.000753

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

714

AN:

68020

Other (OTH)

AF:

0.0881

AC:

186

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

624

1248

1872

2496

3120

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0161

Hom.:

Bravo

AF:

0.126

Asia WGS

AF:

0.143

AC:

498

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.61

PhyloP100

-0.11

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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