dbSNP rs11024460: ENSG00000302464:n.97-2413C>T (chr11-18062635-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000787024.1(ENSG00000302464):n.97-2413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,110 control chromosomes in the GnomAD database, including 3,029 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 0.18 ( 3029 hom., cov: 32)

Consequence

ENSG00000302464
ENST00000787024.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.828

Publications

7 publications found

Variant links:

Genes affected

ENSG00000302464 (HGNC:):

ENSG00000302464 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302464	ENST00000787024.1 link	n.97-2413C>T	intron_variant	Intron 1 of 1
ENSG00000302464	ENST00000787025.1 link	n.194+601C>T	intron_variant	Intron 2 of 2
ENSG00000302464	ENST00000787026.1 link	n.190+601C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26664

AN:

151992

Hom.:

3029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0527

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.0196

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.184

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

GnomAD4 genome

AF:

0.175

AC:

26666

AN:

152110

Hom.:

3029

Cov.:

AF XY:

0.176

AC XY:

13075

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.0525

AC:

2180

AN:

41526

American (AMR)

AF:

0.154

AC:

2360

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

653

AN:

3472

East Asian (EAS)

AF:

0.0197

AC:

102

AN:

5188

South Asian (SAS)

AF:

0.135

AC:

650

AN:

4820

European-Finnish (FIN)

AF:

0.283

AC:

2980

AN:

10544

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17002

AN:

67962

Other (OTH)

AF:

0.183

AC:

386

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1069

2137

3206

4274

5343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.210

Hom.:

5509

Bravo

AF:

0.164

Asia WGS

AF:

0.0730

AC:

259

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

0.23

(source)

DANN

Benign

0.59

PhyloP100

-0.83

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