ENST00000663345.2:n.207+1531G>A

Variant names:

• chr3-195076-C-T
• rs1516338
• ENST00000663345.2:n.207+1531G>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+1531G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,040 control chromosomes in the GnomAD database, including 32,676 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 0.64 (32676 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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+1531G>A		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1	n.253+1891G>A		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000757000.1	n.118+1531G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97172 AN: 151924 Hom.: 32656 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.639 AC: 97228 AN: 152040 Hom.: 32676 Cov.: 32 AF XY: 0.648 AC XY: 48155 AN XY: 74330

African (AFR) AF: 0.427 AC: 17699 AN: 41408

American (AMR) AF: 0.701 AC: 10713 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4991 AN: 5180

South Asian (SAS) AF: 0.729 AC: 3515 AN: 4820

European-Finnish (FIN) AF: 0.758 AC: 8016 AN: 10576

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47720 AN: 67988

Other (OTH) AF: 0.638 AC: 1351 AN: 2116

Alfa AF: 0.672 Hom.: 64281

Bravo AF: 0.627

Asia WGS AF: 0.831 AC: 2885 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	1.7
DANN	Benign	0.18
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs1516338; hg19: chr3-236759; COSMIC: COSV56607860;