rs6442427

Variant names:

• chr3-170062-C-T
• rs6442427
• ENST00000663345.2:n.207+26545G>A

Variant summary

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

The ENST00000663345.2(CHL1-AS2):​n.207+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 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 7 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=-0.96).
• 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	ENST00000663345.2	n.207+26545G>A		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1	n.253+26905G>A		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000757000.1	n.118+26545G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.677 AC: 28082 AN: 41466

American (AMR) AF: 0.781 AC: 11945 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2596 AN: 3468

East Asian (EAS) AF: 0.914 AC: 4738 AN: 5182

South Asian (SAS) AF: 0.740 AC: 3563 AN: 4818

European-Finnish (FIN) AF: 0.858 AC: 9097 AN: 10598

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54560 AN: 68014

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.789 Hom.: 209554

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6442427; hg19: chr3-211745;