rs17533090

Variant names:

• chr6-32622945-G-T
• rs17533090
• ENST00000843606.1:n.179C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000843606.1(ENSG00000309733):​n.179C>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 0.16 in 151,814 control chromosomes in the GnomAD database, including 2,054 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 (2054 hom., cov: 33)
• Consequence: ENSG00000309733 ENST00000843606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 45 publications found

Genes affected

ENSG00000309733 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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
ENSG00000309733	ENST00000843606.1	n.179C>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24203 AN: 151694 Hom.: 2049 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.160 AC: 24230 AN: 151814 Hom.: 2054 Cov.: 33 AF XY: 0.161 AC XY: 11930 AN XY: 74218

African (AFR) AF: 0.155 AC: 6397 AN: 41324

American (AMR) AF: 0.145 AC: 2215 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3470

East Asian (EAS) AF: 0.0964 AC: 499 AN: 5174

South Asian (SAS) AF: 0.161 AC: 775 AN: 4804

European-Finnish (FIN) AF: 0.221 AC: 2336 AN: 10568

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10763 AN: 67890

Other (OTH) AF: 0.178 AC: 374 AN: 2104

Alfa AF: 0.155 Hom.: 4797

Bravo AF: 0.153

Asia WGS AF: 0.145 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs17533090; hg19: chr6-32590722;