chr12-12937897-A-G

Position:

• chr12-12937897-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_149067.1(GPRC5D-AS1):​n.78+10094A>G variant causes a intron, non coding transcript 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 NR_149067.1 intron, non_coding_transcript
• 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 Benign. Variant got -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/exons	MANE	Protein	UniProt
GPRC5D-AS1	NR_149067.1	n.78+10094A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPRC5D-AS1	ENST00000542078.2	n.70+10094A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.625

Alfa AF: 0.573 Hom.: 34305

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

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;