dbSNP rs12555078: ENSG00000286840:n.269+5279C>T (chr9-73542784-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000667966.1(ENSG00000286840):n.269+5279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 151,980 control chromosomes in the GnomAD database, including 532 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 0.078 ( 532 hom., cov: 32)

Consequence

ENSG00000286840
ENST00000667966.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810

Publications

7 publications found

Variant links:

Genes affected

ENSG00000286840 (HGNC:):

ENSG00000286840 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286840	ENST00000667966.1 link	n.269+5279C>T	intron_variant	Intron 1 of 3
ENSG00000232590	ENST00000715871.1 link	n.182-35085G>A	intron_variant	Intron 2 of 2
ENSG00000232590	ENST00000715872.1 link	n.196-60580G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0783

AC:

11891

AN:

151862

Hom.:

532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0879

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.0459

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0491

Gnomad FIN

AF:

0.0563

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0765

Gnomad OTH

AF:

0.0705

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

GnomAD4 genome

AF:

0.0783

AC:

11894

AN:

151980

Hom.:

532

Cov.:

AF XY:

0.0778

AC XY:

5782

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.0878

AC:

3640

AN:

41436

American (AMR)

AF:

0.119

AC:

1817

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0459

AC:

159

AN:

3464

East Asian (EAS)

AF:

0.000388

AC:

AN:

5160

South Asian (SAS)

AF:

0.0482

AC:

232

AN:

4818

European-Finnish (FIN)

AF:

0.0563

AC:

595

AN:

10568

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0765

AC:

5201

AN:

67970

Other (OTH)

AF:

0.0697

AC:

147

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

566

1131

1697

2262

2828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0756

Hom.:

519

Bravo

AF:

0.0807

Asia WGS

AF:

0.0300

AC:

105

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.2

(source)

DANN

Benign

0.54

PhyloP100

-0.081

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