rs9843107

Positions:

• chr3-6644516-G-A

Variant summary

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

The ENST00000433639.1(ENSG00000189229):​n.195-73053G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,202 control chromosomes in the GnomAD database, including 1,141 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 0.11 (1141 hom., cov: 32)
• Consequence: ENSG00000189229 ENST00000433639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

ENSG00000189229 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRM7-AS3	NR_110123.1	n.151-9319C>T		intron_variant
LOC105376944	NR_188693.1	n.232-50261G>A		intron_variant
LOC105376944	NR_188694.1	n.232-50209G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000189229	ENST00000433639.1	n.195-73053G>A		intron_variant		1
ENSG00000189229	ENST00000342990.4	n.146-50213G>A		intron_variant		3
GRM7-AS3	ENST00000412629.6	n.181-9319C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16930 AN: 152084 Hom.: 1137 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.111 AC: 16959 AN: 152202 Hom.: 1141 Cov.: 32 AF XY: 0.115 AC XY: 8594 AN XY: 74424

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0957

Gnomad4 NFE AF: 0.0719

Gnomad4 OTH AF: 0.111

Alfa AF: 0.101 Hom.: 193

Bravo AF: 0.121

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9843107; hg19: chr3-6686203;