6-30820414-T-C

Variant names:

• chr6-30820414-T-C
• rs3094111
• ENST00000399196.1:n.146-5642A>G

Variant summary

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

The ENST00000399196.1(LINC00243):​n.146-5642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,178 control chromosomes in the GnomAD database, including 48,355 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 0.79 (48355 hom., cov: 32)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 23 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.146-5642A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000399196.1	n.146-5642A>G		intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.7	n.145+10101A>G		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.128-5642A>G		intron_variant	Intron 1 of 2
LINC00243	ENST00000719490.1	n.206+8826A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120466 AN: 152060 Hom.: 48323 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.792 AC: 120552 AN: 152178 Hom.: 48355 Cov.: 32 AF XY: 0.796 AC XY: 59228 AN XY: 74380

African (AFR) AF: 0.661 AC: 27435 AN: 41484

American (AMR) AF: 0.821 AC: 12573 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3181 AN: 3470

East Asian (EAS) AF: 0.957 AC: 4954 AN: 5178

South Asian (SAS) AF: 0.830 AC: 3999 AN: 4818

European-Finnish (FIN) AF: 0.884 AC: 9380 AN: 10610

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56288 AN: 67994

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.816 Hom.: 144875

Bravo AF: 0.783

Asia WGS AF: 0.893 AC: 3107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.86
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs3094111; hg19: chr6-30788191;