rs10510181

chr3-149364-G-Achr3-149364-G-T

Variant summary

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

The ENST00000663345.1(CHL1-AS2):n.116-33427C>T 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 0.313 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 ENST00000663345.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHL1-AS2	ENST00000663345.1	n.116-33427C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.320

Alfa AF: 0.336 Hom.: 13570

Bravo AF: 0.303

Asia WGS AF: 0.312 AC: 1082 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510181; hg19: chr3-191047;