rs6485999

Variant names:

• chr11-49637434-G-C
• rs6485999
• ENST00000527477.1:n.1062+60528G>C

Variant summary

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

The ENST00000527477.1(GRM5P1):​n.1062+60528G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,034 control chromosomes in the GnomAD database, including 19,794 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 0.49 (19794 hom., cov: 33)
• Consequence: GRM5P1 ENST00000527477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRM5P1	NR_027044.1	n.1049+60528G>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRM5P1	ENST00000527477.1	n.1062+60528G>C		intron_variant	Intron 2 of 6	1
GRM5P1	ENST00000530858.5	n.1062+60528G>C		intron_variant	Intron 2 of 6	6
GRM5P1	ENST00000534201.5	n.1031+60528G>C		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74134 AN: 151916 Hom.: 19780 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.488 AC: 74168 AN: 152034 Hom.: 19794 Cov.: 33 AF XY: 0.490 AC XY: 36370 AN XY: 74280

African (AFR) AF: 0.259 AC: 10718 AN: 41462

American (AMR) AF: 0.608 AC: 9283 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2865 AN: 5164

South Asian (SAS) AF: 0.502 AC: 2419 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5977 AN: 10566

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38558 AN: 67948

Other (OTH) AF: 0.548 AC: 1159 AN: 2116

Alfa AF: 0.529 Hom.: 2780

Bravo AF: 0.485

Asia WGS AF: 0.485 AC: 1685 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6485999; hg19: chr11-49658986;