9-89683253-C-T

Variant names:

• chr9-89683253-C-T
• rs4077800
• ENST00000617436.3:n.1417+9766C>T

Variant summary

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

The ENST00000617436.3(LINC03062):​n.1417+9766C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 150,550 control chromosomes in the GnomAD database, including 2,866 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 0.18 (2866 hom., cov: 31)
• Consequence: LINC03062 ENST00000617436.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 4 publications found

Genes affected

LINC03062 (HGNC:56369): (long intergenic non-protein coding RNA 3062)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000617436.3. 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
	LINC03062	NR_024280.1		n.1383+9766C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03062	ENST00000617436.3	TSL:2	n.1417+9766C>T		intron	N/A
	LINC03062	ENST00000718835.1		n.302-13560C>T		intron	N/A
	LINC03062	ENST00000718836.1		n.138-14780C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26583 AN: 150494 Hom.: 2866 Cov.: 31

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.305

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.177 AC: 26587 AN: 150550 Hom.: 2866 Cov.: 31 AF XY: 0.174 AC XY: 12752 AN XY: 73306

African (AFR) AF: 0.0719 AC: 2949 AN: 41022

American (AMR) AF: 0.151 AC: 2283 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3462

East Asian (EAS) AF: 0.0307 AC: 157 AN: 5122

South Asian (SAS) AF: 0.175 AC: 837 AN: 4778

European-Finnish (FIN) AF: 0.217 AC: 2156 AN: 9936

Middle Eastern (MID) AF: 0.308 AC: 88 AN: 286

European-Non Finnish (NFE) AF: 0.245 AC: 16622 AN: 67794

Other (OTH) AF: 0.211 AC: 441 AN: 2090

Alfa AF: 0.224 Hom.: 2113

Bravo AF: 0.167

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.43
PhyloP100		0.24

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: rs4077800;

hg19: chr9-92298168;