Variant 3-128928-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000657108.1(CHL1-AS2):n.150+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
ENST00000657108.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Variant links:

Genes affected

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

CHL1-AS2 links:

ENSG00000287140 (HGNC:):

ENSG00000287140 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC107986057	XR_001740581.1 link	n.310+530C>G	intron_variant
LOC107986057	XR_001740582.2 link	n.310+530C>G	intron_variant
LOC107986057	XR_001740583.1 link	n.339+530C>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
CHL1-AS2	ENST00000657108.1 link	n.150+2268G>C	intron_variant
CHL1-AS2	ENST00000663345.1 link	n.116-12991G>C	intron_variant
ENSG00000287140	ENST00000671279.1 link	n.153-678C>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47856

AN:

151596

Hom.:

8284

Cov.:

show subpopulations

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.:

AF XY:

0.320

AC XY:

23705

AN XY:

74098

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.317

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.61

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over