rs12192704

Variant names:

• chr6-30824493-G-A
• rs12192704
• ENST00000399196.1:n.145+6022C>T

Variant summary

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

The ENST00000399196.1(LINC00243):​n.145+6022C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,762 control chromosomes in the GnomAD database, including 1,310 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 0.11 (1310 hom., cov: 31)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 17 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.145+6022C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000399196.1	n.145+6022C>T		intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.7	n.145+6022C>T		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.127+6022C>T		intron_variant	Intron 1 of 2
LINC00243	ENST00000719490.1	n.206+4747C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16802 AN: 151652 Hom.: 1310 Cov.: 31

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0777

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

GnomAD4 genome AF: 0.111 AC: 16808 AN: 151762 Hom.: 1310 Cov.: 31 AF XY: 0.115 AC XY: 8529 AN XY: 74102

African (AFR) AF: 0.0254 AC: 1052 AN: 41412

American (AMR) AF: 0.0952 AC: 1449 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3464

East Asian (EAS) AF: 0.225 AC: 1163 AN: 5162

South Asian (SAS) AF: 0.125 AC: 603 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2533 AN: 10434

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9514 AN: 67944

Other (OTH) AF: 0.0798 AC: 168 AN: 2104

Alfa AF: 0.121 Hom.: 3453

Bravo AF: 0.0937

Asia WGS AF: 0.211 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.78
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12192704; hg19: chr6-30792270;