rs345233

Positions:

• chr3-6729065-T-C

Variant summary

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

The NR_110123.1(GRM7-AS3):​n.150+61988A>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 0.259 in 152,072 control chromosomes in the GnomAD database, including 5,448 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 0.26 (5448 hom., cov: 32)
• Consequence: GRM7-AS3 NR_110123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

GRM7-AS3 (HGNC:42444): (GRM7 antisense RNA 3)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRM7-AS3	NR_110123.1	n.150+61988A>G		intron_variant, non_coding_transcript_variant
LOC105376944	XR_007095803.1	n.1821-3206T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRM7-AS3	ENST00000412629.6	n.180+61988A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000655754.1	n.602-3206T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39367 AN: 151954 Hom.: 5435 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.259 AC: 39391 AN: 152072 Hom.: 5448 Cov.: 32 AF XY: 0.260 AC XY: 19318 AN XY: 74352

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.269

Alfa AF: 0.229 Hom.: 3925

Bravo AF: 0.263

Asia WGS AF: 0.235 AC: 814 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.99
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs345233; hg19: chr3-6770752;