rs4752220

Variant names:

• chr10-118856097-A-G
• rs4752220
• ENST00000663084.1:n.396+10090T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-118856097-A-G
• chr10-118856097-A-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.423+10090T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,026 control chromosomes in the GnomAD database, including 13,473 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 0.41 (13473 hom., cov: 32)
• Consequence: LINC03036 NR_186540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 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.423+10090T>C		intron	N/A
	LINC03036	NR_186541.1		n.499+10090T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000663084.1		n.396+10090T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62222 AN: 151908 Hom.: 13475 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.409 AC: 62234 AN: 152026 Hom.: 13473 Cov.: 32 AF XY: 0.414 AC XY: 30756 AN XY: 74302

African (AFR) AF: 0.260 AC: 10774 AN: 41478

American (AMR) AF: 0.494 AC: 7549 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2211 AN: 5162

South Asian (SAS) AF: 0.391 AC: 1879 AN: 4810

European-Finnish (FIN) AF: 0.539 AC: 5695 AN: 10558

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30979 AN: 67962

Other (OTH) AF: 0.413 AC: 874 AN: 2114

Alfa AF: 0.422 Hom.: 4125

Bravo AF: 0.405

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs4752220; hg19: chr10-120615609;