rs2249349

Variant names:

• chr10-53020917-C-T
• rs2249349
• ENST00000654808.1:n.251+1907G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_186376.1(LINC02672):​n.356+1907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,026 control chromosomes in the GnomAD database, including 20,345 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 0.50 (20345 hom., cov: 32)
• Consequence: LINC02672 NR_186376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

Genes affected

LINC02672 (HGNC:54159): (long intergenic non-protein coding RNA 2672)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186376.1. 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
	LINC02672	NR_186376.1		n.356+1907G>A		intron	N/A
	LINC02672	NR_186377.1		n.356+1907G>A		intron	N/A
	LINC02672	NR_186378.1		n.337+1907G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02672	ENST00000654808.1		n.251+1907G>A		intron	N/A
	LINC02672	ENST00000668157.1		n.270+1907G>A		intron	N/A
	LINC02672	ENST00000718647.1		n.389+1907G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75768 AN: 151908 Hom.: 20338 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75798 AN: 152026 Hom.: 20345 Cov.: 32 AF XY: 0.503 AC XY: 37340 AN XY: 74292

African (AFR) AF: 0.268 AC: 11114 AN: 41478

American (AMR) AF: 0.596 AC: 9101 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2845 AN: 5150

South Asian (SAS) AF: 0.644 AC: 3103 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6263 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39578 AN: 67980

Other (OTH) AF: 0.525 AC: 1106 AN: 2106

Alfa AF: 0.559 Hom.: 18569

Bravo AF: 0.486

Asia WGS AF: 0.600 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs2249349; hg19: chr10-54780677;