rs12446448

Variant names:

• chr16-65148161-G-A
• rs12446448
• ENST00000563754.3:n.557-6062C>T

Variant summary

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

The ENST00000563754.3(LINC02126):​n.557-6062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,074 control chromosomes in the GnomAD database, including 6,011 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 0.26 (6011 hom., cov: 32)
• Consequence: LINC02126 ENST00000563754.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 3 publications found

Genes affected

LINC02126 (HGNC:52983): (long intergenic non-protein coding RNA 2126)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02126	NR_110918.1	n.407-6062C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02126	ENST00000563754.3	n.557-6062C>T		intron_variant	Intron 3 of 3	1
LINC02126	ENST00000765102.1	n.567-11786C>T		intron_variant	Intron 3 of 3
LINC02126	ENST00000765103.1	n.475-6178C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39238 AN: 151956 Hom.: 6011 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.258 AC: 39251 AN: 152074 Hom.: 6011 Cov.: 32 AF XY: 0.257 AC XY: 19074 AN XY: 74328

African (AFR) AF: 0.113 AC: 4712 AN: 41518

American (AMR) AF: 0.187 AC: 2855 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3472

East Asian (EAS) AF: 0.137 AC: 706 AN: 5164

South Asian (SAS) AF: 0.280 AC: 1352 AN: 4820

European-Finnish (FIN) AF: 0.322 AC: 3401 AN: 10574

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24325 AN: 67960

Other (OTH) AF: 0.248 AC: 524 AN: 2110

Alfa AF: 0.286 Hom.: 1216

Bravo AF: 0.238

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.47
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12446448; hg19: chr16-65182064;