chr12-47837647-G-A

Variant names:

• chr12-47837647-G-A
• rs12721364
• ENST00000548564.1:n.493-171G>A

Variant summary

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

The ENST00000548564.1(LINC02354):​n.493-171G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,274 control chromosomes in the GnomAD database, including 1,805 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 0.12 (1805 hom., cov: 33)
• Consequence: LINC02354 ENST00000548564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 28 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02354	XR_001749114.2	n.519-171G>A		intron_variant	Intron 2 of 2
LINC02354	XR_007063292.1	n.788-171G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02354	ENST00000548564.1	n.493-171G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18759 AN: 152156 Hom.: 1804 Cov.: 33

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.123 AC: 18753 AN: 152274 Hom.: 1805 Cov.: 33 AF XY: 0.127 AC XY: 9420 AN XY: 74456

African (AFR) AF: 0.0274 AC: 1139 AN: 41568

American (AMR) AF: 0.0803 AC: 1229 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 330 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2572 AN: 5182

South Asian (SAS) AF: 0.177 AC: 855 AN: 4828

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10353 AN: 68000

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.139 Hom.: 3675

Bravo AF: 0.113

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12721364; hg19: chr12-48231430;