rs4843359

Variant names:

• chr16-86243835-G-A
• rs4843359
• ENST00000597373.2:n.333-17058C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-86243835-G-A
• chr16-86243835-G-C

Variant summary

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

The ENST00000602425.2(LINC01081):​n.465-17058C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,300 control chromosomes in the GnomAD database, including 987 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 0.073 (987 hom., cov: 33)
• Consequence: LINC01081 ENST00000602425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

Genes affected

LINC01081 (HGNC:49124): (long intergenic non-protein coding RNA 1081)

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602425.2. 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
	LINC01081	NR_104139.1		n.395-17058C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01081	ENST00000597373.2	TSL:5	n.333-17058C>T		intron	N/A
	LINC01081	ENST00000602425.2	TSL:2	n.465-17058C>T		intron	N/A
	LINC01081	ENST00000806422.1		n.480-17058C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11131 AN: 152182 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0733 AC: 11160 AN: 152300 Hom.: 987 Cov.: 33 AF XY: 0.0804 AC XY: 5990 AN XY: 74462

African (AFR) AF: 0.0469 AC: 1949 AN: 41572

American (AMR) AF: 0.167 AC: 2552 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2371 AN: 5162

South Asian (SAS) AF: 0.112 AC: 543 AN: 4828

European-Finnish (FIN) AF: 0.0786 AC: 835 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0360 AC: 2449 AN: 68024

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0483 Hom.: 462

Bravo AF: 0.0829

Asia WGS AF: 0.258 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.52
PhyloP100		-1.1

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: rs4843359;

hg19: chr16-86277441;