rs1264362

Positions:

• chr6-30808813-C-G

Variant summary

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

The ENST00000419357.6(LINC00243):​n.146-10041G>C 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 0.228 in 152,154 control chromosomes in the GnomAD database, including 4,709 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 0.23 (4709 hom., cov: 32)
• Consequence: LINC00243 ENST00000419357.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-10041G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34723 AN: 152036 Hom.: 4701 Cov.: 32

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.228 AC: 34747 AN: 152154 Hom.: 4709 Cov.: 32 AF XY: 0.230 AC XY: 17068 AN XY: 74368

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0742

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.229

Alfa AF: 0.281 Hom.: 3740

Bravo AF: 0.210

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264362; hg19: chr6-30776590;