6-30826840-T-C

Variant names:

• chr6-30826840-T-C
• rs915664
• ENST00000399196.1:n.145+3675A>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+3675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,178 control chromosomes in the GnomAD database, including 5,048 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 0.24 (5048 hom., cov: 33)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.145+3675A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000399196.1	n.145+3675A>G		intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.7	n.145+3675A>G		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.127+3675A>G		intron_variant	Intron 1 of 2
LINC00243	ENST00000719490.1	n.206+2400A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36771 AN: 152060 Hom.: 5039 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36779 AN: 152178 Hom.: 5048 Cov.: 33 AF XY: 0.242 AC XY: 18028 AN XY: 74384

African (AFR) AF: 0.136 AC: 5646 AN: 41550

American (AMR) AF: 0.217 AC: 3316 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3464

East Asian (EAS) AF: 0.0649 AC: 337 AN: 5190

South Asian (SAS) AF: 0.184 AC: 888 AN: 4824

European-Finnish (FIN) AF: 0.373 AC: 3946 AN: 10566

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20793 AN: 67984

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.278 Hom.: 25578

Bravo AF: 0.227

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.35
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs915664; hg19: chr6-30794617;