rs10805321

Variant names:

• chr4-13912749-C-A
• rs10805321
• ENST00000503532.1:n.231-47240C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-13912749-C-A
• chr4-13912749-C-T

Variant summary

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

The ENST00000503532.1(LINC01182):​n.231-47240C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,006 control chromosomes in the GnomAD database, including 2,225 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 0.17 (2225 hom., cov: 32)
• Consequence: LINC01182 ENST00000503532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 8 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ENSG00000306343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503532.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	NR_121681.1		n.350-16601C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	ENST00000503532.1	TSL:4	n.231-47240C>A		intron	N/A
	LINC01182	ENST00000510907.5	TSL:2	n.350-16601C>A		intron	N/A
	LINC01182	ENST00000669061.1		n.713+74290C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25602 AN: 151886 Hom.: 2215 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.169 AC: 25632 AN: 152006 Hom.: 2225 Cov.: 32 AF XY: 0.173 AC XY: 12882 AN XY: 74284

African (AFR) AF: 0.143 AC: 5937 AN: 41452

American (AMR) AF: 0.203 AC: 3095 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.183 AC: 945 AN: 5164

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1810 AN: 10550

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11109 AN: 67964

Other (OTH) AF: 0.200 AC: 421 AN: 2106

Alfa AF: 0.166 Hom.: 8122

Bravo AF: 0.167

Asia WGS AF: 0.242 AC: 841 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.5
DANN	Benign	0.91
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10805321; hg19: chr4-13914373;