rs12364577

Variant names:

• chr11-49685809-A-C
• rs12364577
• ENST00000527477.1:n.1063-98014A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000527477.1(GRM5P1):​n.1063-98014A>C variant causes a intron 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 ENST00000527477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942
• Publications: 7 publications found

Genes affected

GRM5P1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GRM5P1	NR_027044.1	n.1050-98014A>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRM5P1	ENST00000527477.1	n.1063-98014A>C		intron_variant	Intron 2 of 6	1
GRM5P1	ENST00000530858.5	n.1063-98014A>C		intron_variant	Intron 2 of 6	6
GRM5P1	ENST00000534201.5	n.1032-98014A>C		intron_variant	Intron 2 of 6	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

African (AFR) AF: 0.0892 AC: 3698 AN: 41468

American (AMR) AF: 0.507 AC: 7682 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2003 AN: 3462

East Asian (EAS) AF: 0.326 AC: 1664 AN: 5100

South Asian (SAS) AF: 0.298 AC: 1432 AN: 4812

European-Finnish (FIN) AF: 0.463 AC: 4882 AN: 10536

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30606 AN: 67684

Other (OTH) AF: 0.416 AC: 873 AN: 2098

Alfa AF: 0.427 Hom.: 7115

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs12364577; hg19: chr11-49707361;