rs163968

Variant names:

• chr3-6753803-C-T
• rs163968
• ENST00000412629.7:n.184+37250G>A

Variant summary

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

The ENST00000412629.7(GRM7-AS3):​n.184+37250G>A variant causes a intron 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 ENST00000412629.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GRM7-AS3	NR_110123.1	n.150+37250G>A		intron_variant	Intron 2 of 3
GRM7-AS3	NR_110125.1	n.151-16966G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRM7-AS3	ENST00000412629.7	n.184+37250G>A		intron_variant	Intron 2 of 3	3
GRM7-AS3	ENST00000417482.5	n.140-16966G>A		intron_variant	Intron 2 of 3	3
GRM7-AS3	ENST00000424366.5	n.129-13175G>A		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.102 AC: 4250 AN: 41526

American (AMR) AF: 0.160 AC: 2446 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.0208 AC: 108 AN: 5186

South Asian (SAS) AF: 0.145 AC: 699 AN: 4814

European-Finnish (FIN) AF: 0.191 AC: 2024 AN: 10578

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11847 AN: 67998

Other (OTH) AF: 0.150 AC: 318 AN: 2114

Alfa AF: 0.165 Hom.: 4157

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs163968; hg19: chr3-6795490;