18-40085433-T-C

Variant names:

• chr18-40085433-T-C
• rs8092348
• ENST00000566101.1:n.1004+2661T>C

Variant summary

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

The ENST00000566101.1(LINC01477):​n.1004+2661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,218 control chromosomes in the GnomAD database, including 3,128 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 0.19 (3128 hom., cov: 32)
• Consequence: LINC01477 ENST00000566101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

LINC01477 (HGNC:51119): (long intergenic non-protein coding RNA 1477)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01477	NR_110791.1	n.1004+2661T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01477	ENST00000566101.1	n.1004+2661T>C		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28503 AN: 152100 Hom.: 3105 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28561 AN: 152218 Hom.: 3128 Cov.: 32 AF XY: 0.189 AC XY: 14037 AN XY: 74430

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.185

Alfa AF: 0.161 Hom.: 262

Bravo AF: 0.206

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8092348; hg19: chr18-37665397;