3-148728-A-G

Position:

• chr3-148728-A-G

Variant summary

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

The ENST00000663345.1(CHL1-AS2):​n.116-32791T>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 0.448 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 ENST00000663345.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHL1-AS2	ENST00000663345.1	n.116-32791T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.0608

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.477

Alfa AF: 0.357 Hom.: 1285

Bravo AF: 0.444

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9754552; hg19: chr3-190411;