3-129285-T-G

Position:

• chr3-129285-T-G

Variant summary

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

The ENST00000657108.1(CHL1-AS2):​n.150+1911A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,892 control chromosomes in the GnomAD database, including 11,821 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 0.38 (11821 hom., cov: 32)
• Consequence: CHL1-AS2 ENST00000657108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619

Genes affected

CHL1-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986057	XR_001740581.1	n.311-321T>G		intron_variant
LOC107986057	XR_001740582.2	n.310+887T>G		intron_variant
LOC107986057	XR_001740583.1	n.340-321T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHL1-AS2	ENST00000657108.1	n.150+1911A>C		intron_variant
CHL1-AS2	ENST00000663345.1	n.116-13348A>C		intron_variant
ENSG00000287140	ENST00000671279.1	n.153-321T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56960 AN: 151774 Hom.: 11820 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.375 AC: 56978 AN: 151892 Hom.: 11821 Cov.: 32 AF XY: 0.378 AC XY: 28009 AN XY: 74194

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.384

Alfa AF: 0.425 Hom.: 25939

Bravo AF: 0.363

Asia WGS AF: 0.352 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	8.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400180; hg19: chr3-170968;