dbSNP rs471146: SPECC1P1:n.837T>C (chr17-15860829-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000421102.6(SPECC1P1):n.837T>C variant causes a non coding transcript exon 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: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SPECC1P1
ENST00000421102.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.861

Publications

1 publications found

Variant links:

Genes affected

SPECC1P1 (HGNC:53867): (SPECC1 pseudogene 1)

SPECC1P1 links:

ENSG00000290377 (HGNC:):

ENSG00000290377 links:

ADORA2B (HGNC:264): (adenosine A2b receptor) This gene encodes an adenosine receptor that is a member of the G protein-coupled receptor superfamily. This integral membrane protein stimulates adenylate cyclase activity in the presence of adenosine. This protein also interacts with netrin-1, which is involved in axon elongation. The gene is located near the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

ADORA2B links:

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ACMG classification

Classification was made for transcript

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=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA2B	XM_047435373.1 link	c.-481+2011T>C		intron_variant	Intron 3 of 5		XP_047291329.1
ADORA2B	XM_047435374.1 link	c.-657T>C		upstream_gene_variant			XP_047291330.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SPECC1P1	ENST00000421102.6 link	n.837T>C	non_coding_transcript_exon_variant	Exon 7 of 9	6
ENSG00000290377	ENST00000784729.1 link	n.155-3226T>C	intron_variant	Intron 1 of 2
ENSG00000290377	ENST00000784730.1 link	n.310+2011T>C	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

29272

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17178

African (AFR)

AF:

0.00

AC:

AN:

718

American (AMR)

AF:

0.00

AC:

AN:

3392

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

440

East Asian (EAS)

AF:

0.00

AC:

AN:

2064

South Asian (SAS)

AF:

0.00

AC:

AN:

3030

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2052

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1616

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

14604

Other (OTH)

AF:

0.00

AC:

AN:

1356

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.5

(source)

DANN

Benign

0.35

PhyloP100

0.86

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