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:

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new If you want to explore the variant's impact on the transcript ENST00000489253.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over