Genetic Variant ENSG00000291185:n.549+5539A>G (chr9-15120191-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 ENST00000609203.1(ENSG00000291185):n.549+5539A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,186 control chromosomes in the GnomAD database, including 1,109 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 ( 1109 hom., cov: 32)

Consequence

ENSG00000291185
ENST00000609203.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

3 publications found

Variant links:

Genes affected

ENSG00000291185 (HGNC:):

ENSG00000291185 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291185	ENST00000609203.1 link	n.549+5539A>G	intron_variant	Intron 2 of 9	2
ENSG00000291185	ENST00000759520.1 link	n.97+22794A>G	intron_variant	Intron 1 of 3
ENSG00000291185	ENST00000759521.1 link	n.318+25754A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17466

AN:

152068

Hom.:

1101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0975

Gnomad OTH

AF:

0.102

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

GnomAD4 genome

AF:

0.115

AC:

17489

AN:

152186

Hom.:

1109

Cov.:

AF XY:

0.117

AC XY:

8698

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.118

AC:

4913

AN:

41534

American (AMR)

AF:

0.170

AC:

2602

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0455

AC:

158

AN:

3470

East Asian (EAS)

AF:

0.209

AC:

1083

AN:

5170

South Asian (SAS)

AF:

0.154

AC:

744

AN:

4820

European-Finnish (FIN)

AF:

0.101

AC:

1066

AN:

10598

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0975

AC:

6628

AN:

67988

Other (OTH)

AF:

0.109

AC:

230

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

778

1556

2335

3113

3891

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.113

Hom.:

499

Bravo

AF:

0.124

Asia WGS

AF:

0.197

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.77

(source)

DANN

Benign

0.51

PhyloP100

-0.040

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