6-30804601-A-G

Variant names:

• chr6-30804601-A-G
• rs3094123
• ENST00000419357.7:n.146-5829T>C

Variant summary

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

The ENST00000419357.7(LINC00243):​n.146-5829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,168 control chromosomes in the GnomAD database, including 55,562 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 0.85 (55562 hom., cov: 32)
• Consequence: LINC00243 ENST00000419357.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 27 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.7	n.146-5829T>C		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.498-5829T>C		intron_variant	Intron 2 of 2
LINC00243	ENST00000719490.1	n.207-5829T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129777 AN: 152050 Hom.: 55514 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.854 AC: 129881 AN: 152168 Hom.: 55562 Cov.: 32 AF XY: 0.857 AC XY: 63766 AN XY: 74392

African (AFR) AF: 0.838 AC: 34762 AN: 41484

American (AMR) AF: 0.863 AC: 13189 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3191 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5021 AN: 5186

South Asian (SAS) AF: 0.948 AC: 4567 AN: 4816

European-Finnish (FIN) AF: 0.885 AC: 9377 AN: 10596

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56884 AN: 68008

Other (OTH) AF: 0.850 AC: 1798 AN: 2116

Alfa AF: 0.847 Hom.: 198536

Bravo AF: 0.851

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.58
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3094123; hg19: chr6-30772378;