rs12375908

Variant names:

• chr9-87012187-C-A
• rs12375908
• ENST00000602579.1:n.257-1977G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-87012187-C-A
• chr9-87012187-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000602579.1(LINC02893):​n.257-1977G>T variant causes a intron change. The variant allele was found at a frequency of 0.00000189 in 1,057,366 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: LINC02893 ENST00000602579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.61
• Publications: 0 publications found

Genes affected

LINC02893 (HGNC:55359): (long intergenic non-protein coding RNA 2893)

CDC20P1 (HGNC:29487): (cell division cycle 20 pseudogene 1)

GAS1RR (HGNC:52261): (GAS1 adjacent regulatory RNA)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC20P1		n.87012187C>A		intragenic_variant
LINC02893	NR_027471.1	n.257-1977G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02893	ENST00000602579.1	n.257-1977G>T		intron_variant	Intron 1 of 1	1
CDC20P1	ENST00000488829.1	n.536C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
GAS1RR	ENST00000846239.1	n.921C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000189 AC: 2 AN: 1057366 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 544170

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 25790

American (AMR) AF: 0.00 AC: 0 AN: 44248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23588

East Asian (EAS) AF: 0.00 AC: 0 AN: 37886

South Asian (SAS) AF: 0.00 AC: 0 AN: 78118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52980

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4976

European-Non Finnish (NFE) AF: 0.00000269 AC: 2 AN: 742788

Other (OTH) AF: 0.00 AC: 0 AN: 46992

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		5.6

Splicing

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

Other links and lift over

dbSNP: rs12375908; hg19: chr9-89627102;