chr12-12937897-A-C

Variant names:

• chr12-12937897-A-C
• rs704225
• ENST00000536029.1:n.40+10094A>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000543515.8(GPRC5D-AS1):​n.92+10094A>C variant causes a intron 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)
• Consequence: GPRC5D-AS1 ENST00000543515.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

GPRC5D-AS1 (HGNC:53599): (GPRC5D and HEBP1 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPRC5D-AS1	NR_149062.1	n.78+10094A>C		intron_variant	Intron 1 of 2
GPRC5D-AS1	NR_149063.1	n.78+10094A>C		intron_variant	Intron 1 of 3
GPRC5D-AS1	NR_149064.1	n.78+10094A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPRC5D-AS1	ENST00000536029.1	n.40+10094A>C		intron_variant	Intron 1 of 3	3
GPRC5D-AS1	ENST00000540198.1	n.78-6475A>C		intron_variant	Intron 1 of 3	5
GPRC5D-AS1	ENST00000542078.2	n.70+10094A>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704225; hg19: chr12-13090831;