Genetic Variant ENSG00000230472:n.-164G>C (chr6-50637569-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000750353.1(ENSG00000230472):n.-164G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,890 control chromosomes in the GnomAD database, including 5,102 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 0.21 ( 5102 hom., cov: 32)

Consequence

ENSG00000230472
ENST00000750353.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.478

Publications

0 publications found

Variant links:

Genes affected

ENSG00000230472 (HGNC:):

ENSG00000230472 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 (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000230472	ENST00000750353.1 link	n.-164G>C	upstream_gene_variant
ENSG00000230472	ENST00000750354.1 link	n.-173G>C	upstream_gene_variant
ENSG00000230472	ENST00000750355.1 link	n.-208G>C	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31588

AN:

151772

Hom.:

5080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.00755

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0993

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.187

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

GnomAD4 genome

AF:

0.208

AC:

31649

AN:

151890

Hom.:

5102

Cov.:

AF XY:

0.204

AC XY:

15144

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.459

AC:

19002

AN:

41384

American (AMR)

AF:

0.133

AC:

2033

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

622

AN:

3468

East Asian (EAS)

AF:

0.00757

AC:

AN:

5152

South Asian (SAS)

AF:

0.124

AC:

595

AN:

4800

European-Finnish (FIN)

AF:

0.0993

AC:

1049

AN:

10568

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.114

AC:

7747

AN:

67956

Other (OTH)

AF:

0.184

AC:

388

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1121

2241

3362

4482

5603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0628

Hom.:

Bravo

AF:

0.221

Asia WGS

AF:

0.0870

AC:

303

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

6.1

(source)

DANN

Benign

0.48

PhyloP100

0.48

Splicing

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

Publications

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chr6-50637569-C-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