Genetic Variant ENSG00000299150:n.328+15474C>G (chr11-121353175-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000761170.1(ENSG00000299150):n.328+15474C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,014 control chromosomes in the GnomAD database, including 2,208 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 0.15 ( 2208 hom., cov: 31)

Consequence

ENSG00000299150
ENST00000761170.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.585

Publications

4 publications found

Variant links:

Genes affected

ENSG00000299150 (HGNC:):

ENSG00000299150 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299150	ENST00000761170.1 link	n.328+15474C>G	intron_variant	Intron 1 of 2
ENSG00000299150	ENST00000761171.1 link	n.216-15183C>G	intron_variant	Intron 1 of 4
ENSG00000299150	ENST00000761172.1 link	n.197+15474C>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23414

AN:

151896

Hom.:

2206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.0837

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.154

AC:

23443

AN:

152014

Hom.:

2208

Cov.:

AF XY:

0.154

AC XY:

11415

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.268

AC:

11117

AN:

41446

American (AMR)

AF:

0.148

AC:

2252

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.0837

AC:

290

AN:

3466

East Asian (EAS)

AF:

0.166

AC:

857

AN:

5158

South Asian (SAS)

AF:

0.129

AC:

620

AN:

4824

European-Finnish (FIN)

AF:

0.103

AC:

1092

AN:

10576

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.100

AC:

6831

AN:

67974

Other (OTH)

AF:

0.135

AC:

284

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

956

1912

2867

3823

4779

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.0423

Hom.:

Bravo

AF:

0.161

Asia WGS

AF:

0.149

AC:

518

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.78

(source)

DANN

Benign

0.70

PhyloP100

-0.58

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