dbSNP rs9890278: ENSG00000250838:n.402A>G (chr17-48996587-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 ENST00000766836.1(ENSG00000250838):n.402A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,272 control chromosomes in the GnomAD database, including 32,620 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 0.65 ( 32582 hom., cov: 32)

Exomes 𝑓: 0.61 ( 38 hom. )

Consequence

ENSG00000250838
ENST00000766836.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Publications

2 publications found

Variant links:

Genes affected

ENSG00000250838 (HGNC:):

ENSG00000250838 links:

IGF2BP1 (HGNC:28866): (insulin like growth factor 2 mRNA binding protein 1) This gene encodes a member of the insulin-like growth factor 2 mRNA-binding protein family. The protein encoded by this gene contains four K homology domains and two RNA recognition motifs. It functions by binding to the mRNAs of certain genes, including insulin-like growth factor 2, beta-actin and beta-transducin repeat-containing protein, and regulating their translation. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

IGF2BP1 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF2BP1	XM_047435139.1 link	c.-763T>C		5_prime_UTR_variant	Exon 1 of 16		XP_047291095.1
IGF2BP1	XM_011524201.3 link	c.-536T>C		5_prime_UTR_variant	Exon 1 of 17		XP_011522503.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000250838	ENST00000766836.1 link	n.402A>G	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000250838	ENST00000505903.1 link	n.38-96A>G	intron_variant	Intron 1 of 2	3
ENSG00000250838	ENST00000766827.1 link	n.195-1005A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.646

AC:

98236

AN:

151958

Hom.:

32527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.801

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.572

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.615

GnomAD4 exome

AF:

0.607

AC:

119

AN:

196

Hom.:

AF XY:

0.592

AC XY:

AN XY:

142

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.833

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.462

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.610

AC:

AN:

154

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.647

AC:

98354

AN:

152076

Hom.:

32582

Cov.:

AF XY:

0.644

AC XY:

47908

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.801

AC:

33257

AN:

41498

American (AMR)

AF:

0.643

AC:

9832

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.572

AC:

1986

AN:

3470

East Asian (EAS)

AF:

0.656

AC:

3374

AN:

5140

South Asian (SAS)

AF:

0.565

AC:

2724

AN:

4818

European-Finnish (FIN)

AF:

0.573

AC:

6065

AN:

10592

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.577

AC:

39184

AN:

67946

Other (OTH)

AF:

0.618

AC:

1307

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1748

3495

5243

6990

8738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.563

Hom.:

9746

Bravo

AF:

0.657

Asia WGS

AF:

0.652

AC:

2269

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

(source)

DANN

Benign

0.68

PhyloP100

0.10

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over