ENST00000489253.1:n.352T>A

Variant names:

• chr10-89979068-T-A
• rs11812465
• ENST00000489253.1:n.352T>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000489253.1(SNRPD2P1):​n.352T>A variant causes a splice region, non coding transcript exon change. 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNRPD2P1 ENST00000489253.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.36
• Publications: 4 publications found

Genes affected

SNRPD2P1 (HGNC:31459): (small nuclear ribonucleoprotein D2 pseudogene 1)

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489253.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPD2P1	ENST00000489253.1	TSL:6	n.352T>A		splice_region non_coding_transcript_exon	Exon 1 of 1
	LINC00865	ENST00000664430.1		n.548+64298T>A		intron	N/A
	LINC00865	ENST00000715760.1		n.741-40767T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 528890 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 286046

African (AFR) AF: 0.00 AC: 0 AN: 15084

American (AMR) AF: 0.00 AC: 0 AN: 33210

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15194

East Asian (EAS) AF: 0.00 AC: 0 AN: 33766

South Asian (SAS) AF: 0.00 AC: 0 AN: 53672

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3680

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 301532

Other (OTH) AF: 0.00 AC: 0 AN: 28306

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 3915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		5.4

Splicing

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

Other links and lift over

dbSNP: rs11812465; hg19: chr10-91738825;