dbSNP rs12547784: ENSG00000286798:n.-31T>C (chr8-13629594-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000668622.2(ENSG00000286798):n.-31T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 152,144 control chromosomes in the GnomAD database, including 902 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 0.095 ( 902 hom., cov: 32)

Consequence

ENSG00000286798
ENST00000668622.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286798 (HGNC:):

ENSG00000286798 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102725080	NR_134450.1 link	n.-96T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000286798	ENST00000668622.2 link	n.-31T>C	upstream_gene_variant
ENSG00000286798	ENST00000811223.1 link	n.-43T>C	upstream_gene_variant
ENSG00000286798	ENST00000811224.1 link	n.-50T>C	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0951

AC:

14458

AN:

152026

Hom.:

902

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0583

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0725

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.0951

AC:

14470

AN:

152144

Hom.:

902

Cov.:

AF XY:

0.0996

AC XY:

7408

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0584

AC:

2428

AN:

41542

American (AMR)

AF:

0.197

AC:

3005

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

496

AN:

3468

East Asian (EAS)

AF:

0.153

AC:

788

AN:

5154

South Asian (SAS)

AF:

0.0724

AC:

349

AN:

4822

European-Finnish (FIN)

AF:

0.107

AC:

1134

AN:

10590

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0880

AC:

5987

AN:

68012

Other (OTH)

AF:

0.108

AC:

228

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

651

1303

1954

2606

3257

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0841

Hom.:

Bravo

AF:

0.103

Asia WGS

AF:

0.105

AC:

363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.57

PhyloP100

-0.23

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