3-6729065-T-C

Variant names:

• chr3-6729065-T-C
• rs345233
• ENST00000433639.1:n.391-3206T>C

Variant summary

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

The ENST00000433639.1(ENSG00000189229):​n.391-3206T>C variant causes a intron 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: ENSG00000189229 ENST00000433639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

Genes affected

ENSG00000189229 (HGNC:):

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=-0.97).
• 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 rank	MANE	Protein	UniProt
GRM7-AS3	NR_110123.1	n.150+61988A>G		intron_variant	Intron 2 of 3
LOC105376944	NR_188693.1	n.529-3206T>C		intron_variant	Intron 4 of 5
LOC105376944	NR_188694.1	n.581-3206T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000189229	ENST00000433639.1	n.391-3206T>C		intron_variant	Intron 3 of 4	1
ENSG00000189229	ENST00000342990.4	n.491-3206T>C		intron_variant	Intron 4 of 5	3
GRM7-AS3	ENST00000412629.7	n.184+61988A>G		intron_variant	Intron 2 of 3	3

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

African (AFR) AF: 0.362 AC: 15009 AN: 41474

American (AMR) AF: 0.198 AC: 3021 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3464

East Asian (EAS) AF: 0.269 AC: 1388 AN: 5168

South Asian (SAS) AF: 0.258 AC: 1246 AN: 4832

European-Finnish (FIN) AF: 0.208 AC: 2200 AN: 10580

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14734 AN: 67958

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.234 Hom.: 5328

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs345233; hg19: chr3-6770752;