rs1516350

Variant names:

• chr3-152931-A-G
• rs1516350
• ENST00000663345.2:n.208-36994T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-152931-A-G
• chr3-152931-A-T

Variant summary

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

The ENST00000663345.2(CHL1-AS2):​n.208-36994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,020 control chromosomes in the GnomAD database, including 34,460 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 0.67 (34460 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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.208-36994T>C		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1	n.254-36994T>C		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000757000.1	n.119-40471T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101967 AN: 151902 Hom.: 34431 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.671 AC: 102046 AN: 152020 Hom.: 34460 Cov.: 32 AF XY: 0.670 AC XY: 49753 AN XY: 74282

African (AFR) AF: 0.615 AC: 25536 AN: 41490

American (AMR) AF: 0.659 AC: 10062 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2324 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2878 AN: 5170

South Asian (SAS) AF: 0.592 AC: 2843 AN: 4802

European-Finnish (FIN) AF: 0.722 AC: 7610 AN: 10546

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48581 AN: 67970

Other (OTH) AF: 0.671 AC: 1414 AN: 2108

Alfa AF: 0.695 Hom.: 61095

Bravo AF: 0.664

Asia WGS AF: 0.560 AC: 1946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1516350; hg19: chr3-194614;