chr6-30830214-C-T

Variant names:

• chr6-30830214-C-T
• rs7749924
• ENST00000719502.1:n.374G>A

Variant summary

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

The ENST00000719502.1(LINC00243):​n.374G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,118 control chromosomes in the GnomAD database, including 1,127 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 0.12 (1127 hom., cov: 31)
• Consequence: LINC00243 ENST00000719502.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.145+301G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000719502.1	n.374G>A		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00243	ENST00000399196.1	n.145+301G>A		intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.7	n.145+301G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18063 AN: 152000 Hom.: 1120 Cov.: 31

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18085 AN: 152118 Hom.: 1127 Cov.: 31 AF XY: 0.120 AC XY: 8887 AN XY: 74360

African (AFR) AF: 0.0893 AC: 3698 AN: 41434

American (AMR) AF: 0.140 AC: 2141 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.174 AC: 904 AN: 5182

South Asian (SAS) AF: 0.148 AC: 714 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10594

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8441 AN: 68010

Other (OTH) AF: 0.127 AC: 268 AN: 2108

Alfa AF: 0.121 Hom.: 4068

Bravo AF: 0.120

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.6
DANN	Benign	0.82
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7749924; hg19: chr6-30797991;