chr6-30802955-T-G

Variant names:

• chr6-30802955-T-G
• rs13198118
• ENST00000419357.6:n.146-4183A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419357.6(LINC00243):​n.146-4183A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,968 control chromosomes in the GnomAD database, including 3,014 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 0.17 (3014 hom., cov: 30)
• Consequence: LINC00243 ENST00000419357.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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	ENST00000419357.6	n.146-4183A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26492 AN: 151850 Hom.: 3009 Cov.: 30

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.175 AC: 26521 AN: 151968 Hom.: 3014 Cov.: 30 AF XY: 0.182 AC XY: 13518 AN XY: 74262

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.203

Alfa AF: 0.175 Hom.: 4418

Bravo AF: 0.183

Asia WGS AF: 0.393 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13198118; hg19: chr6-30770732;