rs9890278

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000505903.1(ENSG00000250838):​n.38-96A>G variant causes a intron, non coding transcript 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


ENST00000505903.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
IGF2BP1XM_011524201.3 linkuse as main transcriptc.-536T>C 5_prime_UTR_variant 1/17
IGF2BP1XM_047435139.1 linkuse as main transcriptc.-763T>C 5_prime_UTR_variant 1/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000505903.1 linkuse as main transcriptn.38-96A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.646
AC:
98236
AN:
151958
Hom.:
32527
Cov.:
32
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.:
38
AF XY:
0.592
AC XY:
84
AN XY:
142
show subpopulations
Gnomad4 AMR exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.833
Gnomad4 FIN exome
AF:
0.462
Gnomad4 NFE exome
AF:
0.610
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.647
AC:
98354
AN:
152076
Hom.:
32582
Cov.:
32
AF XY:
0.644
AC XY:
47908
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.801
Gnomad4 AMR
AF:
0.643
Gnomad4 ASJ
AF:
0.572
Gnomad4 EAS
AF:
0.656
Gnomad4 SAS
AF:
0.565
Gnomad4 FIN
AF:
0.573
Gnomad4 NFE
AF:
0.577
Gnomad4 OTH
AF:
0.618
Alfa
AF:
0.543
Hom.:
4513
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
12
DANN
Benign
0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9890278; hg19: chr17-47073949; API