6-30817496-T-C

Position:

• chr6-30817496-T-C

Variant summary

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

The NR_130726.1(LINC00243):​n.146-2724A>G 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 0.179 in 152,238 control chromosomes in the GnomAD database, including 3,107 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 (3107 hom., cov: 32)
• Consequence: LINC00243 NR_130726.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00243	NR_130726.1	n.146-2724A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00243	ENST00000419357.6	n.145+13019A>G		intron_variant, non_coding_transcript_variant		3
LINC00243	ENST00000399196.1	n.146-2724A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27223 AN: 152120 Hom.: 3102 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.179 AC: 27252 AN: 152238 Hom.: 3107 Cov.: 32 AF XY: 0.187 AC XY: 13924 AN XY: 74440

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.205

Alfa AF: 0.180 Hom.: 5048

Bravo AF: 0.186

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713380; hg19: chr6-30785273;