18-40085433-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566101.1. 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
	LINC01477	NR_110791.1		n.1004+2661T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01477	ENST00000566101.1	TSL:1	n.1004+2661T>C		intron	N/A

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

African (AFR) AF: 0.250 AC: 10363 AN: 41526

American (AMR) AF: 0.285 AC: 4366 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1938 AN: 5168

South Asian (SAS) AF: 0.156 AC: 754 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1185 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8910 AN: 68020

Other (OTH) AF: 0.185 AC: 389 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.0040

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: rs8092348;

hg19: chr18-37665397;