rs754059

Variant names:

• chr10-118810998-G-A
• rs754059
• ENST00000663084.1:n.397-23956C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-118810998-G-A
• chr10-118810998-G-C
• chr10-118810998-G-T

Variant summary

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

The NR_186540.1(LINC03036):​n.424-23956C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,152 control chromosomes in the GnomAD database, including 29,954 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 0.63 (29954 hom., cov: 34)
• Consequence: LINC03036 NR_186540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 0 publications found

Genes affected

LINC03036 (HGNC:56220): (long intergenic non-protein coding RNA 3036)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186540.1. 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
	LINC03036	NR_186540.1		n.424-23956C>T		intron	N/A
	LINC03036	NR_186541.1		n.500-23956C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000663084.1		n.397-23956C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95211 AN: 152034 Hom.: 29927 Cov.: 34

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.626 AC: 95291 AN: 152152 Hom.: 29954 Cov.: 34 AF XY: 0.624 AC XY: 46384 AN XY: 74366

African (AFR) AF: 0.686 AC: 28475 AN: 41536

American (AMR) AF: 0.634 AC: 9700 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2844 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2845 AN: 4830

European-Finnish (FIN) AF: 0.580 AC: 6122 AN: 10556

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40787 AN: 67976

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.609 Hom.: 14811

Bravo AF: 0.632

Asia WGS AF: 0.600 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs754059; hg19: chr10-120570510;