3-117400-G-A

Variant names:

• chr3-117400-G-A
• rs17033096
• ENST00000657108.2:n.157-1463C>T

Variant summary

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

The ENST00000657108.2(CHL1-AS2):​n.157-1463C>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 ENST00000657108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657108.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000657108.2		n.157-1463C>T		intron	N/A
	CHL1-AS2	ENST00000663345.2		n.208-1463C>T		intron	N/A
	CHL1-AS2	ENST00000756999.1		n.254-1463C>T		intron	N/A

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

African (AFR) AF: 0.311 AC: 12852 AN: 41266

American (AMR) AF: 0.143 AC: 2184 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3472

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5176

South Asian (SAS) AF: 0.234 AC: 1122 AN: 4804

European-Finnish (FIN) AF: 0.136 AC: 1431 AN: 10542

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12486 AN: 67968

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.185 Hom.: 3372

Bravo AF: 0.212

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.63
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs17033096; hg19: chr3-159083;