rs9295917

Variant names:

• chr6-30801995-C-G
• rs9295917
• ENST00000419357.7:n.146-3223G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419357.7(LINC00243):​n.146-3223G>C variant causes a intron 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 ENST00000419357.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.7	n.146-3223G>C		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.498-3223G>C		intron_variant	Intron 2 of 2
LINC00243	ENST00000719490.1	n.207-3223G>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0929 AC: 3860 AN: 41536

American (AMR) AF: 0.304 AC: 4639 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2277 AN: 5158

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4822

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10584

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10571 AN: 68004

Other (OTH) AF: 0.203 AC: 427 AN: 2108

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
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs9295917; hg19: chr6-30769772;