rs9469300

Variant names:

• chr6-32892975-G-A
• rs9469300
• ENST00000688327.2:n.*222C>T

Variant summary

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

The ENST00000688327.2(ENSG00000289559):​n.*222C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,072 control chromosomes in the GnomAD database, including 1,457 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 0.13 (1457 hom., cov: 32)
• Consequence: ENSG00000289559 ENST00000688327.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

Genes affected

ENSG00000289559 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289559	ENST00000688327.2	n.*222C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19598 AN: 151956 Hom.: 1451 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.129 AC: 19642 AN: 152072 Hom.: 1457 Cov.: 32 AF XY: 0.130 AC XY: 9639 AN XY: 74328

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.120

Alfa AF: 0.106 Hom.: 1493

Bravo AF: 0.128

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9469300; hg19: chr6-32860752;