3-148728-A-G

Variant names:

• chr3-148728-A-G
• rs9754552
• ENST00000663345.2:n.208-32791T>C

Variant summary

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

The ENST00000663345.2(CHL1-AS2):​n.208-32791T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,986 control chromosomes in the GnomAD database, including 16,297 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 (16297 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000663345.2		n.208-32791T>C		intron	N/A
	CHL1-AS2	ENST00000756999.1		n.254-32791T>C		intron	N/A
	CHL1-AS2	ENST00000757000.1		n.119-36268T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68100 AN: 151868 Hom.: 16290 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.0609

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.448 AC: 68145 AN: 151986 Hom.: 16297 Cov.: 32 AF XY: 0.442 AC XY: 32820 AN XY: 74266

African (AFR) AF: 0.354 AC: 14690 AN: 41464

American (AMR) AF: 0.399 AC: 6082 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2156 AN: 3468

East Asian (EAS) AF: 0.0608 AC: 314 AN: 5162

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4814

European-Finnish (FIN) AF: 0.426 AC: 4502 AN: 10560

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36619 AN: 67954

Other (OTH) AF: 0.477 AC: 1003 AN: 2104

Alfa AF: 0.358 Hom.: 1333

Bravo AF: 0.444

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.20
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9754552; hg19: chr3-190411;