rs4684083

chr3-147182-T-C

Variant summary

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

The XR_007095782.1(LOC124909336):n.203T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,136 control chromosomes in the GnomAD database, including 4,620 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 0.24 (4620 hom., cov: 32)
• Consequence: LOC124909336 XR_007095782.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

LOC124909336 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909336	XR_007095782.1	n.203T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHL1-AS2	ENST00000663345.1	n.116-31245A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36740 AN: 152018 Hom.: 4619 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.242 AC: 36761 AN: 152136 Hom.: 4620 Cov.: 32 AF XY: 0.241 AC XY: 17930 AN XY: 74378

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0525

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.249

Alfa AF: 0.273 Hom.: 3204

Bravo AF: 0.240

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4684083; hg19: chr3-188865;