6-30817496-T-C

Variant names:

• chr6-30817496-T-C
• rs4713380
• ENST00000399196.1:n.146-2724A>G

Variant summary

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

The ENST00000399196.1(LINC00243):​n.146-2724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,238 control chromosomes in the GnomAD database, including 3,107 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 0.18 (3107 hom., cov: 32)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 32 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399196.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00243	NR_130726.1		n.146-2724A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00243	ENST00000399196.1	TSL:2	n.146-2724A>G		intron	N/A
	LINC00243	ENST00000419357.7	TSL:3	n.145+13019A>G		intron	N/A
	LINC00243	ENST00000719489.1		n.128-2724A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27223 AN: 152120 Hom.: 3102 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.179 AC: 27252 AN: 152238 Hom.: 3107 Cov.: 32 AF XY: 0.187 AC XY: 13924 AN XY: 74440

African (AFR) AF: 0.0963 AC: 4000 AN: 41546

American (AMR) AF: 0.306 AC: 4671 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2261 AN: 5180

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4826

European-Finnish (FIN) AF: 0.155 AC: 1644 AN: 10610

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 10987 AN: 68012

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.176 Hom.: 11091

Bravo AF: 0.186

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4713380;

hg19: chr6-30785273;