5-6584135-T-C

Variant names:

• chr5-6584135-T-C
• rs7735244
• ENST00000507582.3:n.70+1424T>C

Variant summary

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

The ENST00000507582.3(LINC01018):​n.70+1424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 152,052 control chromosomes in the GnomAD database, including 584 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 0.080 (584 hom., cov: 32)
• Consequence: LINC01018 ENST00000507582.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 6 publications found

Genes affected

LINC01018 (HGNC:27394): (long intergenic non-protein coding RNA 1018)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507582.3. 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
	LINC01018	NR_024423.2		n.512+334T>C		intron	N/A
	LINC01018	NR_024424.2		n.526+334T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01018	ENST00000507582.3	TSL:1	n.70+1424T>C		intron	N/A
	LINC01018	ENST00000505626.7	TSL:2	n.513+334T>C		intron	N/A
	LINC01018	ENST00000507628.2	TSL:4	n.665+334T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12124 AN: 151932 Hom.: 586 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0797 AC: 12121 AN: 152052 Hom.: 584 Cov.: 32 AF XY: 0.0787 AC XY: 5847 AN XY: 74318

African (AFR) AF: 0.0371 AC: 1538 AN: 41480

American (AMR) AF: 0.0820 AC: 1252 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.183 AC: 946 AN: 5164

South Asian (SAS) AF: 0.0717 AC: 345 AN: 4814

European-Finnish (FIN) AF: 0.0583 AC: 616 AN: 10564

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6772 AN: 67978

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0911 Hom.: 1807

Bravo AF: 0.0822

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.94
DANN	Benign	0.83
PhyloP100		0.45

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: rs7735244;

hg19: chr5-6584248;