rs9295888

Variant names:

• chr6-30454704-G-A
• rs9295888
• ENST00000658719.1:n.1688G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-30454704-G-A
• chr6-30454704-G-T

Variant summary

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

The ENST00000658719.1(ENSG00000286301):​n.1688G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,092 control chromosomes in the GnomAD database, including 2,227 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 0.16 (2227 hom., cov: 32)
• Consequence: ENSG00000286301 ENST00000658719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

Genes affected

ENSG00000286301 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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
ENSG00000286301	ENST00000658719.1	n.1688G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24868 AN: 151974 Hom.: 2227 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.164 AC: 24883 AN: 152092 Hom.: 2227 Cov.: 32 AF XY: 0.159 AC XY: 11809 AN XY: 74370

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0315

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.152

Alfa AF: 0.129 Hom.: 520

Bravo AF: 0.171

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295888; hg19: chr6-30422481;