Variant rs2292832 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The NM_002081.3(GPC1):c.167-2944T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes 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: 35)

Consequence

GPC1
NM_002081.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.770

Links

GPC1 (HGNC:4449):

MIR149 (HGNC:31536):

GPC1-AS1 (HGNC:56102):

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 35.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
GPC1	NM_002081.3 linkuse as main transcript	c.167-2944T>A	intron_variant		ENST00000264039.7
MIR149	NR_029702.1 linkuse as main transcript	n.86T>A	non_coding_transcript_exon_variant	1/1
GPC1-AS1	NR_161169.1 linkuse as main transcript	n.104+511A>T	intron_variant, non_coding_transcript_variant
GPC1	XM_047443961.1 linkuse as main transcript	c.-202T>A	5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPC1	ENST00000264039.7 linkuse as main transcript	c.167-2944T>A	intron_variant		1	NM_002081.3	P1	P35052-1
MIR149	ENST00000384879.1 linkuse as main transcript	n.86T>A	non_coding_transcript_exon_variant	1/1
GPC1-AS1	ENST00000404327.3 linkuse as main transcript	n.118+511A>T	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

Cadd

Benign

9.4

Dann

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over