dbSNP rs887357: ENSG00000291189:n.64+580T>G (chr12-3365479-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000636557.1(ENSG00000291189):n.64+580T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,230 control chromosomes in the GnomAD database, including 2,283 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 0.16 ( 2283 hom., cov: 33)

Consequence

ENSG00000291189
ENST00000636557.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.362

Publications

3 publications found

Variant links:

Genes affected

ENSG00000291189 (HGNC:):

ENSG00000291189 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128253	NR_148995.1 link	n.64+580T>G		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291189	ENST00000636557.1 link	n.64+580T>G	intron_variant	Intron 1 of 5	5
ENSG00000291189	ENST00000637529.1 link	n.54+580T>G	intron_variant	Intron 1 of 7	5
ENSG00000291189	ENST00000685534.2 link	n.89+580T>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24849

AN:

152112

Hom.:

2280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0903

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.173

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

GnomAD4 genome

AF:

0.163

AC:

24882

AN:

152230

Hom.:

2283

Cov.:

AF XY:

0.161

AC XY:

11981

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.183

AC:

7596

AN:

41532

American (AMR)

AF:

0.127

AC:

1937

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

1102

AN:

3472

East Asian (EAS)

AF:

0.000967

AC:

AN:

5170

South Asian (SAS)

AF:

0.0912

AC:

440

AN:

4822

European-Finnish (FIN)

AF:

0.202

AC:

2143

AN:

10602

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11069

AN:

68008

Other (OTH)

AF:

0.172

AC:

363

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1052

2104

3156

4208

5260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.165

Hom.:

4313

Bravo

AF:

0.161

Asia WGS

AF:

0.0480

AC:

169

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.2

(source)

DANN

Benign

0.80

PhyloP100

0.36

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