rs3842755
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NR_003512.4(INS-IGF2):n.246+1219G>T 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 0.172 in 152,172 control chromosomes in the GnomAD database, including 2,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2425 hom., cov: 32)
Consequence
INS-IGF2
NR_003512.4 intron, non_coding_transcript
NR_003512.4 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.76
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 11-2159566-C-A is Benign according to our data. Variant chr11-2159566-C-A is described in ClinVar as [Benign]. Clinvar id is 1275239.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INS-IGF2 | NR_003512.4 | n.246+1219G>T | intron_variant, non_coding_transcript_variant | |||||
INS-IGF2 | NM_001042376.3 | c.187+1219G>T | intron_variant | NP_001035835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.172 AC: 26167AN: 152056Hom.: 2424 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.172 AC: 26167AN: 152172Hom.: 2425 Cov.: 32 AF XY: 0.167 AC XY: 12403AN XY: 74410
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334
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 25, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at