rs965084

Variant names:

• chr3-125415-G-C
• rs965084
• ENST00000657108.2:n.156+5781C>G

Variant summary

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

The ENST00000657108.2(CHL1-AS2):​n.156+5781C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,946 control chromosomes in the GnomAD database, including 8,309 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 0.32 (8309 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000657108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 0 publications found

Genes affected

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

ENSG00000287140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000657108.2		n.156+5781C>G		intron	N/A
	CHL1-AS2	ENST00000663345.2		n.208-9478C>G		intron	N/A
	ENSG00000287140	ENST00000671279.1		n.152+1701G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48248 AN: 151828 Hom.: 8304 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.318 AC: 48276 AN: 151946 Hom.: 8309 Cov.: 32 AF XY: 0.322 AC XY: 23906 AN XY: 74228

African (AFR) AF: 0.207 AC: 8568 AN: 41480

American (AMR) AF: 0.376 AC: 5723 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3462

East Asian (EAS) AF: 0.469 AC: 2418 AN: 5156

South Asian (SAS) AF: 0.274 AC: 1317 AN: 4804

European-Finnish (FIN) AF: 0.433 AC: 4567 AN: 10546

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23834 AN: 67944

Other (OTH) AF: 0.314 AC: 663 AN: 2114

Alfa AF: 0.340 Hom.: 1167

Bravo AF: 0.307

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.60
PhyloP100		-0.91

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs965084;

hg19: chr3-167098;