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GeneBe

rs13387042

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The XR_923878.3(LOC105373874):n.7422A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes 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: 33)

Consequence

LOC105373874
XR_923878.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.265

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105373874XR_923878.3 linkuse as main transcriptn.7422A>C non_coding_transcript_exon_variant 3/3
IGFBP-AS1XR_001739169.1 linkuse as main transcriptn.11844+47091A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DIRC3-AS1ENST00000695932.1 linkuse as main transcriptn.509+47091A>C intron_variant, non_coding_transcript_variant
DIRC3-AS1ENST00000695934.1 linkuse as main transcriptn.172+47091A>C intron_variant, non_coding_transcript_variant
DIRC3-AS1ENST00000695937.1 linkuse as main transcriptn.289+3829A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
0.99
Dann
Benign
0.45

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: rs13387042; hg19: chr2-217905832; API