rs1919008

Variant names:

• chr3-107110485-A-C
• rs1919008
• ENST00000484698.5:n.295+19403T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-107110485-A-C
• chr3-107110485-A-T

Variant summary

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

The ENST00000484698.5(LINC00882):​n.295+19403T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,162 control chromosomes in the GnomAD database, including 53,981 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 0.84 (53980 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC00882 ENST00000484698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 1 publications found

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484698.5. 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
	LINC00882	NR_028303.1		n.389-481T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00882	ENST00000484698.5	TSL:1	n.295+19403T>G		intron	N/A
	LINC00882	ENST00000477210.7	TSL:2	n.569-481T>G		intron	N/A
	LINC00882	ENST00000606742.5	TSL:3	n.166+107T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127635 AN: 152044 Hom.: 53955 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.834

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.839 AC: 127694 AN: 152160 Hom.: 53980 Cov.: 32 AF XY: 0.843 AC XY: 62676 AN XY: 74380

African (AFR) AF: 0.730 AC: 30296 AN: 41484

American (AMR) AF: 0.868 AC: 13256 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5174

South Asian (SAS) AF: 0.945 AC: 4559 AN: 4824

European-Finnish (FIN) AF: 0.909 AC: 9634 AN: 10602

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59056 AN: 68010

Other (OTH) AF: 0.837 AC: 1766 AN: 2110

Alfa AF: 0.812 Hom.: 17561

Bravo AF: 0.831

Asia WGS AF: 0.951 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		1.1

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: rs1919008;

hg19: chr3-106829332;