rs345235

Positions:

• chr3-6728622-G-A

Variant summary

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

The ENST00000433639.1(ENSG00000189229):​n.391-3649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,970 control chromosomes in the GnomAD database, including 2,588 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 0.18 (2588 hom., cov: 32)
• Consequence: ENSG00000189229 ENST00000433639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

ENSG00000189229 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRM7-AS3	NR_110123.1	n.150+62431C>T		intron_variant
LOC105376944	NR_188693.1	n.529-3649G>A		intron_variant
LOC105376944	NR_188694.1	n.581-3649G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000189229	ENST00000433639.1	n.391-3649G>A		intron_variant		1
ENSG00000189229	ENST00000342990.4	n.491-3649G>A		intron_variant		3
GRM7-AS3	ENST00000412629.6	n.180+62431C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26937 AN: 151850 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.177 AC: 26941 AN: 151970 Hom.: 2588 Cov.: 32 AF XY: 0.178 AC XY: 13222 AN XY: 74270

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0969

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.211

Alfa AF: 0.201 Hom.: 1525

Bravo AF: 0.173

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs345235; hg19: chr3-6770309;