rs230669

Variant summary

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

The NR_102280.1(KCTD21-AS1):​n.506-9060A>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: 32)

Consequence

KCTD21-AS1
NR_102280.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.946
Variant links:
Genes affected
KCTD21-AS1 (HGNC:48674): (KCTD21 antisense RNA 1)

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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=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCTD21-AS1NR_102280.1 linkuse as main transcriptn.506-9060A>C intron_variant, non_coding_transcript_variant
KCTD21-AS1NR_102281.1 linkuse as main transcriptn.398-9480A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCTD21-AS1ENST00000662186.1 linkuse as main transcriptn.408-9060A>C intron_variant, non_coding_transcript_variant
KCTD21-AS1ENST00000523626.6 linkuse as main transcriptn.398-9480A>C intron_variant, non_coding_transcript_variant 4
KCTD21-AS1ENST00000530261.2 linkuse as main transcriptn.504-9060A>C intron_variant, non_coding_transcript_variant 4
KCTD21-AS1ENST00000663331.1 linkuse as main transcriptn.248-9060A>C intron_variant, non_coding_transcript_variant

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
-0.89
CADD
Benign
0.19
DANN
Benign
0.75

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: rs230669; hg19: chr11-77875386; API