3-149364-G-A

Variant names:

• chr3-149364-G-A
• rs10510181
• ENST00000663345.2:n.208-33427C>T

Variant summary

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

The ENST00000663345.2(CHL1-AS2):​n.208-33427C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,112 control chromosomes in the GnomAD database, including 8,207 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 0.31 (8207 hom., cov: 33)
• Consequence: CHL1-AS2 ENST00000663345.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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.208-33427C>T		intron	N/A
	CHL1-AS2	ENST00000756999.1		n.254-33427C>T		intron	N/A
	CHL1-AS2	ENST00000757000.1		n.119-36904C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47607 AN: 151992 Hom.: 8203 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.313 AC: 47632 AN: 152112 Hom.: 8207 Cov.: 33 AF XY: 0.318 AC XY: 23637 AN XY: 74356

African (AFR) AF: 0.193 AC: 8009 AN: 41520

American (AMR) AF: 0.382 AC: 5840 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2514 AN: 5168

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4563 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23670 AN: 67984

Other (OTH) AF: 0.320 AC: 676 AN: 2112

Alfa AF: 0.330 Hom.: 28679

Bravo AF: 0.303

Asia WGS AF: 0.312 AC: 1082 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.72
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs10510181; hg19: chr3-191047;