chr3-148607-T-C

Variant names:

• chr3-148607-T-C
• rs9754850
• ENST00000663345.2:n.208-32670A>G

Variant summary

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

The ENST00000663345.2(CHL1-AS2):​n.208-32670A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,984 control chromosomes in the GnomAD database, including 15,495 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 0.43 (15495 hom., cov: 33)
• Consequence: CHL1-AS2 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 1 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=-0.6).
• 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000663345.2		n.208-32670A>G		intron	N/A
	CHL1-AS2	ENST00000756999.1		n.254-32670A>G		intron	N/A
	CHL1-AS2	ENST00000757000.1		n.119-36147A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65641 AN: 151866 Hom.: 15496 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.432 AC: 65670 AN: 151984 Hom.: 15495 Cov.: 33 AF XY: 0.426 AC XY: 31648 AN XY: 74264

African (AFR) AF: 0.298 AC: 12361 AN: 41434

American (AMR) AF: 0.395 AC: 6030 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.0611 AC: 316 AN: 5174

South Asian (SAS) AF: 0.427 AC: 2054 AN: 4806

European-Finnish (FIN) AF: 0.426 AC: 4497 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36594 AN: 67974

Other (OTH) AF: 0.461 AC: 972 AN: 2110

Alfa AF: 0.514 Hom.: 9964

Bravo AF: 0.425

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.8
DANN	Benign	0.69
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9754850; hg19: chr3-190290;