3-160351-T-C

Variant names:

• chr3-160351-T-C
• rs1516348
• ENST00000663345.1:n.115+36256A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663345.1(CHL1-AS2):​n.115+36256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,040 control chromosomes in the GnomAD database, including 15,946 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 0.45 (15946 hom., cov: 33)
• Consequence: CHL1-AS2 ENST00000663345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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+36256A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68456 AN: 151922 Hom.: 15950 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.450 AC: 68472 AN: 152040 Hom.: 15946 Cov.: 33 AF XY: 0.443 AC XY: 32948 AN XY: 74298

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.471

Alfa AF: 0.446 Hom.: 2592

Bravo AF: 0.455

Asia WGS AF: 0.262 AC: 913 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	1.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1516348; hg19: chr3-202034;