ENST00000549905.5:n.553+1644A>C

Variant names:

• chr12-74192430-T-G
• rs10506701
• ENST00000549905.5:n.553+1644A>C

Variant summary

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

The ENST00000549905.5(LINC02882):​n.553+1644A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,188 control chromosomes in the GnomAD database, including 2,192 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 0.15 (2192 hom., cov: 32)
• Consequence: LINC02882 ENST00000549905.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 11 publications found

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02882	NR_038300.1	n.553+1644A>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02882	ENST00000549905.5	n.553+1644A>C		intron_variant	Intron 4 of 6	1
LINC02882	ENST00000653134.1	n.634-34546A>C		intron_variant	Intron 6 of 8
LINC02882	ENST00000662107.2	n.505-34546A>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23330 AN: 152070 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.153 AC: 23335 AN: 152188 Hom.: 2192 Cov.: 32 AF XY: 0.152 AC XY: 11318 AN XY: 74376

African (AFR) AF: 0.0616 AC: 2558 AN: 41546

American (AMR) AF: 0.178 AC: 2718 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3472

East Asian (EAS) AF: 0.0529 AC: 274 AN: 5178

South Asian (SAS) AF: 0.100 AC: 485 AN: 4830

European-Finnish (FIN) AF: 0.213 AC: 2245 AN: 10562

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13733 AN: 68010

Other (OTH) AF: 0.147 AC: 311 AN: 2110

Alfa AF: 0.180 Hom.: 5792

Bravo AF: 0.149

Asia WGS AF: 0.101 AC: 352 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10506701; hg19: chr12-74586210;