dbSNP rs11812465: SNRPD2P1:n.352T>A (chr10-89979068-T-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.36

Publications

4 publications found

Variant links:

Genes affected

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

SNRPD2P1 links:

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

LINC00865 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRPD2P1		n.89979068T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNRPD2P1	ENST00000489253.1 link	n.352T>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00865	ENST00000664430.1 link	n.548+64298T>A	intron_variant	Intron 2 of 3
LINC00865	ENST00000715760.1 link	n.741-40767T>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

528890

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

286046

African (AFR)

AF:

0.00

AC:

AN:

15084

American (AMR)

AF:

0.00

AC:

AN:

33210

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15194

East Asian (EAS)

AF:

0.00

AC:

AN:

33766

South Asian (SAS)

AF:

0.00

AC:

AN:

53672

European-Finnish (FIN)

AF:

0.00

AC:

AN:

44446

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3680

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

301532

Other (OTH)

AF:

0.00

AC:

AN:

28306

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

3915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

5.1

(source)

DANN

Benign

0.65

PhyloP100

5.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over