12-12937897-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536029.1(GPRC5D-AS1):​n.40+10094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,942 control chromosomes in the GnomAD database, including 28,402 homozygotes. 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: 𝑓 0.61 (28402 hom., cov: 31)
• Consequence: GPRC5D-AS1 ENST00000536029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPRC5D-AS1	NR_149062.1	n.78+10094A>G		intron_variant	Intron 1 of 2
GPRC5D-AS1	NR_149063.1	n.78+10094A>G		intron_variant	Intron 1 of 3
GPRC5D-AS1	NR_149064.1	n.78+10094A>G		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>G		intron_variant	Intron 1 of 3	3
GPRC5D-AS1	ENST00000540198.1	n.78-6475A>G		intron_variant	Intron 1 of 3	5
GPRC5D-AS1	ENST00000542078.2	n.70+10094A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91974 AN: 151824 Hom.: 28359 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.606 AC: 92072 AN: 151942 Hom.: 28402 Cov.: 31 AF XY: 0.613 AC XY: 45542 AN XY: 74282

African (AFR) AF: 0.609 AC: 25235 AN: 41434

American (AMR) AF: 0.719 AC: 10972 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3468

East Asian (EAS) AF: 0.926 AC: 4790 AN: 5170

South Asian (SAS) AF: 0.683 AC: 3286 AN: 4812

European-Finnish (FIN) AF: 0.609 AC: 6420 AN: 10546

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37189 AN: 67934

Other (OTH) AF: 0.625 AC: 1321 AN: 2114

Alfa AF: 0.579 Hom.: 48672

Bravo AF: 0.615

Asia WGS AF: 0.802 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.63
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs704225; hg19: chr12-13090831;