rs9295917

chr6-30801995-C-G

Variant summary

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

The ENST00000419357.6(LINC00243):n.146-3223G>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 0.174 in 152,164 control chromosomes in the GnomAD database, including 2,996 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 0.17 (2996 hom., cov: 31)
• Consequence: LINC00243 ENST00000419357.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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.146-3223G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26413 AN: 152046 Hom.: 2992 Cov.: 31

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.174 AC: 26437 AN: 152164 Hom.: 2996 Cov.: 31 AF XY: 0.181 AC XY: 13488 AN XY: 74372

Gnomad4 AFR AF: 0.0929

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.203

Alfa AF: 0.159 Hom.: 293

Bravo AF: 0.182

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295917; hg19: chr6-30769772;