3-121187-A-G

Variant names:

• chr3-121187-A-G
• rs4686327
• ENST00000657108.2:n.157-5250T>C

Variant summary

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

The ENST00000657108.2(CHL1-AS2):​n.157-5250T>C variant causes a intron 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 ENST00000657108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 2 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=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHL1-AS2	ENST00000657108.2	n.157-5250T>C		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000663345.2	n.208-5250T>C		intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1	n.254-5250T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.849 AC: 35227 AN: 41506

American (AMR) AF: 0.862 AC: 13173 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2896 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5147 AN: 5178

South Asian (SAS) AF: 0.856 AC: 4109 AN: 4800

European-Finnish (FIN) AF: 0.875 AC: 9258 AN: 10578

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.833 AC: 56624 AN: 67984

Other (OTH) AF: 0.844 AC: 1782 AN: 2112

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
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs4686327; hg19: chr3-162870;