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. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000286301 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.241 AC: 9993 AN: 41462

American (AMR) AF: 0.106 AC: 1627 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5168

South Asian (SAS) AF: 0.142 AC: 683 AN: 4822

European-Finnish (FIN) AF: 0.0891 AC: 944 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10528 AN: 67980

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.150 Hom.: 3581

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9295888; hg19: chr6-30422481;