6-30828768-T-C

Variant names:

• chr6-30828768-T-C
• rs1264350
• ENST00000399196.1:n.145+1747A>G

Variant summary

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

The ENST00000399196.1(LINC00243):​n.145+1747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,298 control chromosomes in the GnomAD database, including 823 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 0.092 (823 hom., cov: 33)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 28 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 (NFE) allele frequency at 95% confidence interval = 0.132 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.145+1747A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00243	ENST00000399196.1	TSL:2	n.145+1747A>G		intron	N/A
	LINC00243	ENST00000419357.7	TSL:3	n.145+1747A>G		intron	N/A
	LINC00243	ENST00000719489.1		n.127+1747A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13958 AN: 152180 Hom.: 823 Cov.: 33

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0916 AC: 13952 AN: 152298 Hom.: 823 Cov.: 33 AF XY: 0.0842 AC XY: 6270 AN XY: 74484

African (AFR) AF: 0.0650 AC: 2703 AN: 41560

American (AMR) AF: 0.0390 AC: 597 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3470

East Asian (EAS) AF: 0.0194 AC: 101 AN: 5194

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4824

European-Finnish (FIN) AF: 0.0757 AC: 804 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9131 AN: 68006

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.124 Hom.: 4268

Bravo AF: 0.0899

Asia WGS AF: 0.0140 AC: 50 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	4.1
DANN	Benign	0.53
PhyloP100		-0.050

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: rs1264350;

hg19: chr6-30796545;