rs163968

Positions:

• chr3-6753803-C-T

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+37250G>A 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 0.149 in 152,194 control chromosomes in the GnomAD database, including 1,839 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 0.15 (1839 hom., cov: 33)
• Consequence: GRM7-AS3 NR_110123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRM7-AS3	NR_110123.1	n.150+37250G>A		intron_variant, non_coding_transcript_variant
GRM7-AS3	NR_110125.1	n.151-16966G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRM7-AS3	ENST00000412629.6	n.180+37250G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22613 AN: 152076 Hom.: 1841 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.149 AC: 22611 AN: 152194 Hom.: 1839 Cov.: 33 AF XY: 0.148 AC XY: 10992 AN XY: 74386

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.150

Alfa AF: 0.171 Hom.: 3088

Bravo AF: 0.147

Asia WGS AF: 0.0690 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163968; hg19: chr3-6795490;