rs1516350

Positions:

• chr3-152931-A-G
• chr3-152931-A-T

Variant summary

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

The ENST00000663345.1(CHL1-AS2):​n.116-36994T>C variant causes a intron, non coding transcript 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 ENST00000663345.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

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=-0.89).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHL1-AS2	ENST00000663345.1	n.116-36994T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.671

Alfa AF: 0.697 Hom.: 15077

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1516350; hg19: chr3-194614;