rs12364577

Positions:

• chr11-49685809-A-C
• chr11-49685809-A-G

Variant summary

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

The NR_027044.1(GRM5P1):​n.1050-98014A>C 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 0.353 in 151,508 control chromosomes in the GnomAD database, including 11,760 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 0.35 (11760 hom., cov: 31)
• Consequence: GRM5P1 NR_027044.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942

Genes affected

GRM5P1 (HGNC:55419): (GRM5 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRM5P1	NR_027044.1	n.1050-98014A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRM5P1	ENST00000527477.1	n.1063-98014A>C		intron_variant, non_coding_transcript_variant		1
GRM5P1	ENST00000530858.5	n.1063-98014A>C		intron_variant, non_coding_transcript_variant
GRM5P1	ENST00000534201.5	n.1032-98014A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53488 AN: 151390 Hom.: 11751 Cov.: 31

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.353 AC: 53510 AN: 151508 Hom.: 11760 Cov.: 31 AF XY: 0.355 AC XY: 26242 AN XY: 73996

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.416

Alfa AF: 0.424 Hom.: 6300

Bravo AF: 0.350

Asia WGS AF: 0.302 AC: 1047 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12364577; hg19: chr11-49707361;