3-121187-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.116-5250T>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 0.849 in 152,120 control chromosomes in the GnomAD database, including 54,860 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 0.85 (54860 hom., cov: 31)
• Consequence: CHL1-AS2 ENST00000663345.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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.116-5250T>C		intron_variant, non_coding_transcript_variant
CHL1-AS2	ENST00000657108.1	n.151-5250T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128962 AN: 152002 Hom.: 54806 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.849 AC: 129076 AN: 152120 Hom.: 54860 Cov.: 31 AF XY: 0.851 AC XY: 63310 AN XY: 74356

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.844

Alfa AF: 0.825 Hom.: 6712

Bravo AF: 0.848

Asia WGS AF: 0.915 AC: 3180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4686327; hg19: chr3-162870;