rs6442427

Variant names:

• chr3-170062-C-T
• rs6442427
• ENST00000663345.1:n.115+26545G>A

Variant summary

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

The ENST00000663345.1(CHL1-AS2):​n.115+26545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,158 control chromosomes in the GnomAD database, including 45,360 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 0.77 (45360 hom., cov: 33)
• Consequence: CHL1-AS2 ENST00000663345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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	ENST00000663345.1	n.115+26545G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116912 AN: 152040 Hom.: 45342 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.769 AC: 116981 AN: 152158 Hom.: 45360 Cov.: 33 AF XY: 0.770 AC XY: 57317 AN XY: 74390

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.749

Alfa AF: 0.790 Hom.: 98044

Bravo AF: 0.758

Asia WGS AF: 0.784 AC: 2723 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6442427; hg19: chr3-211745;