3-150979421-C-T

Position:

• chr3-150979421-C-T

Variant summary

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

The NR_024066.2(CLRN1-AS1):​n.416+6328C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,130 control chromosomes in the GnomAD database, including 2,798 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 0.18 (2798 hom., cov: 32)
• Consequence: CLRN1-AS1 NR_024066.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

CLRN1-AS1 (HGNC:30895): (CLRN1 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLRN1-AS1	NR_024066.2	n.416+6328C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLRN1-AS1	ENST00000465576.1	n.416+6328C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000469268.1	n.236-22153C>T		intron_variant, non_coding_transcript_variant		4
CLRN1-AS1	ENST00000476886.5	n.124-83505C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27599 AN: 152012 Hom.: 2787 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.182 AC: 27638 AN: 152130 Hom.: 2798 Cov.: 32 AF XY: 0.188 AC XY: 13991 AN XY: 74366

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.186

Alfa AF: 0.145 Hom.: 3489

Bravo AF: 0.186

Asia WGS AF: 0.261 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.099
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16863118; hg19: chr3-150697208;