rs17033096

Variant names:

• chr3-117400-G-A
• rs17033096
• ENST00000657108.1:n.151-1463C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-117400-G-A
• chr3-117400-G-C

Variant summary

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

The ENST00000657108.1(CHL1-AS2):​n.151-1463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,816 control chromosomes in the GnomAD database, including 3,652 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 0.21 (3652 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000657108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
CHL1-AS2	ENST00000657108.1	n.151-1463C>T		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000663345.1	n.116-1463C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31728 AN: 151700 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.209 AC: 31778 AN: 151816 Hom.: 3652 Cov.: 32 AF XY: 0.207 AC XY: 15371 AN XY: 74208

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.201

Alfa AF: 0.178 Hom.: 2290

Bravo AF: 0.212

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17033096; hg19: chr3-159083;