rs1264362

Variant names:

• chr6-30808813-C-G
• rs1264362
• ENST00000419357.7:n.146-10041G>C

Variant summary

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

The ENST00000419357.7(LINC00243):​n.146-10041G>C variant causes a intron 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 ENST00000419357.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 22 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.7	n.146-10041G>C		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.497+5590G>C		intron_variant	Intron 2 of 2
LINC00243	ENST00000719490.1	n.207-10041G>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0969 AC: 4023 AN: 41518

American (AMR) AF: 0.200 AC: 3059 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.0742 AC: 385 AN: 5192

South Asian (SAS) AF: 0.192 AC: 927 AN: 4822

European-Finnish (FIN) AF: 0.374 AC: 3946 AN: 10550

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20575 AN: 68002

Other (OTH) AF: 0.229 AC: 482 AN: 2108

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1264362; hg19: chr6-30776590;