12-47837827-A-G

Variant names:

• chr12-47837827-A-G
• rs7965281
• ENST00000548564.1:n.502A>G

Variant summary

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

The ENST00000548564.1(LINC02354):​n.502A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,034 control chromosomes in the GnomAD database, including 15,867 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 0.45 (15866 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: LINC02354 ENST00000548564.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 17 publications found

Genes affected

LINC02354 (HGNC:53276): (long intergenic non-protein coding RNA 2354)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548564.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02354	ENST00000548564.1	TSL:4	n.502A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68531 AN: 151910 Hom.: 15859 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.454

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

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: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.451 AC: 68573 AN: 152028 Hom.: 15866 Cov.: 32 AF XY: 0.450 AC XY: 33455 AN XY: 74316

African (AFR) AF: 0.386 AC: 15993 AN: 41464

American (AMR) AF: 0.401 AC: 6111 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1775 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1364 AN: 5166

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5350 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34395 AN: 67972

Other (OTH) AF: 0.453 AC: 955 AN: 2106

Alfa AF: 0.382 Hom.: 1882

Bravo AF: 0.439

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7965281; hg19: chr12-48231610;