rs1516348

Variant names:

• chr3-160351-T-C
• rs1516348
• ENST00000663345.2:n.207+36256A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-160351-T-C
• chr3-160351-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663345.2(CHL1-AS2):​n.207+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 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663345.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000663345.2		n.207+36256A>G		intron	N/A
	CHL1-AS2	ENST00000756999.1		n.253+36616A>G		intron	N/A
	CHL1-AS2	ENST00000757000.1		n.118+36256A>G		intron	N/A

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

African (AFR) AF: 0.518 AC: 21517 AN: 41500

American (AMR) AF: 0.390 AC: 5945 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 513 AN: 5170

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4818

European-Finnish (FIN) AF: 0.392 AC: 4141 AN: 10558

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31350 AN: 67952

Other (OTH) AF: 0.471 AC: 994 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1516348; hg19: chr3-202034;