GeneBe

rs682567

Positions:

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.189-74552A>C variant causes a intron, non coding transcript 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: 31)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42
Variant links:
Genes affected

Genome browser will be placed here

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=-0.99).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.142+33653A>C intron_variant, non_coding_transcript_variant
LOC124900354XR_001751517.2 linkuse as main transcriptn.142+33653A>C intron_variant, non_coding_transcript_variant
LOC124900354XR_001751518.3 linkuse as main transcriptn.82+2795A>C intron_variant, non_coding_transcript_variant
LOC124900354XR_007064618.1 linkuse as main transcriptn.143-31199A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.189-74552A>C intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.195+33653A>C intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.189-74552A>C intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.69-74552A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.30
DANN
Benign
0.76

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: rs682567; hg19: chr15-48210354; API