dbSNP rs2043052: ENSG00000286745:n.451-10887C>T (chr5-118592406-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 ENST00000666304.1(ENSG00000286745):n.451-10887C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,020 control chromosomes in the GnomAD database, including 25,645 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 0.56 ( 25645 hom., cov: 32)

Consequence

ENSG00000286745
ENST00000666304.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.456

Publications

4 publications found

Variant links:

Genes affected

ENSG00000286745 (HGNC:):

ENSG00000286745 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286745	ENST00000666304.1 link	n.451-10887C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.559

AC:

84840

AN:

151904

Hom.:

25644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.699

Gnomad AMR

AF:

0.509

Gnomad ASJ

AF:

0.684

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.693

Gnomad OTH

AF:

0.594

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

GnomAD4 genome

AF:

0.558

AC:

84865

AN:

152020

Hom.:

25645

Cov.:

AF XY:

0.550

AC XY:

40875

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.387

AC:

16042

AN:

41452

American (AMR)

AF:

0.508

AC:

7769

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

2373

AN:

3470

East Asian (EAS)

AF:

0.119

AC:

613

AN:

5154

South Asian (SAS)

AF:

0.502

AC:

2416

AN:

4814

European-Finnish (FIN)

AF:

0.613

AC:

6473

AN:

10552

Middle Eastern (MID)

AF:

0.670

AC:

197

AN:

294

European-Non Finnish (NFE)

AF:

0.693

AC:

47110

AN:

67980

Other (OTH)

AF:

0.586

AC:

1237

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1719

3439

5158

6878

8597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

716

1432

2148

2864

3580

<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:

0.644

Hom.:

123831

Bravo

AF:

0.540

Asia WGS

AF:

0.304

AC:

1056

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.1

(source)

DANN

Benign

0.75

PhyloP100

0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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