GeneBe

chr2-111246290-T-A

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The XM_047446748.1(LOC124907867):​c.-2+1858A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

LOC124907867
XM_047446748.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40
Variant links:
Genes affected
MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124907867XM_047446748.1 linkc.-2+1858A>T intron_variant Intron 1 of 1 XP_047302704.1
MIR4435-2HGNR_015395.2 linkn.2470-6294A>T intron_variant Intron 3 of 6
MIR4435-2HGNR_136161.1 linkn.637+1858A>T intron_variant Intron 4 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR4435-2HGENST00000439362.6 linkn.544+1858A>T intron_variant Intron 4 of 5 1
MIR4435-2HGENST00000656416.1 linkn.1812A>T non_coding_transcript_exon_variant Exon 5 of 5
MIR4435-2HGENST00000662384.1 linkn.1694A>T non_coding_transcript_exon_variant Exon 4 of 4

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.37
DANN
Benign
0.41

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-112003867; API