rs965084

Positions:

• chr3-125415-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.150+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 ENST00000657108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

Genes affected

CHL1-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986057	XR_001740581.1	n.123+1701G>C		intron_variant
LOC107986057	XR_001740582.2	n.123+1701G>C		intron_variant
LOC107986057	XR_001740583.1	n.152+1672G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHL1-AS2	ENST00000657108.1	n.150+5781C>G		intron_variant
CHL1-AS2	ENST00000663345.1	n.116-9478C>G		intron_variant
ENSG00000287140	ENST00000671279.1	n.152+1701G>C		intron_variant

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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.314

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965084; hg19: chr3-167098;