3-128928-C-G

Variant names:

• chr3-128928-C-G
• rs1400182
• ENST00000657108.2:n.156+2268G>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.156+2268G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,714 control chromosomes in the GnomAD database, including 8,287 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 0.32 (8287 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000657108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

Genes affected

CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

ENSG00000287140 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657108.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHL1-AS2	ENST00000657108.2		n.156+2268G>C		intron	N/A
	CHL1-AS2	ENST00000663345.2		n.208-12991G>C		intron	N/A
	ENSG00000287140	ENST00000671279.1		n.153-678C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47856 AN: 151596 Hom.: 8284 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.316 AC: 47879 AN: 151714 Hom.: 8287 Cov.: 32 AF XY: 0.320 AC XY: 23705 AN XY: 74098

African (AFR) AF: 0.185 AC: 7673 AN: 41452

American (AMR) AF: 0.380 AC: 5793 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2420 AN: 5128

South Asian (SAS) AF: 0.274 AC: 1311 AN: 4776

European-Finnish (FIN) AF: 0.433 AC: 4539 AN: 10486

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24285 AN: 67868

Other (OTH) AF: 0.317 AC: 669 AN: 2108

Alfa AF: 0.221 Hom.: 592

Bravo AF: 0.305

Asia WGS AF: 0.324 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1400182; hg19: chr3-170611;