12-59548341-T-C

Variant names:

• chr12-59548341-T-C
• rs11533655
• ENST00000719152.1:n.101+21220A>G

Variant summary

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

The ENST00000719152.1(LINC02448):​n.101+21220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 140,322 control chromosomes in the GnomAD database, including 6,076 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 0.19 (6076 hom., cov: 25)
• Consequence: LINC02448 ENST00000719152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 1 publications found

Genes affected

LINC02448 (HGNC:53380): (long intergenic non-protein coding RNA 2448)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02448	ENST00000719152.1	n.101+21220A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 26285 AN: 140202 Hom.: 6071 Cov.: 25

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.187 AC: 26305 AN: 140322 Hom.: 6076 Cov.: 25 AF XY: 0.193 AC XY: 13066 AN XY: 67828

African (AFR) AF: 0.0896 AC: 3501 AN: 39088

American (AMR) AF: 0.241 AC: 3287 AN: 13614

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 654 AN: 3372

East Asian (EAS) AF: 0.676 AC: 3166 AN: 4686

South Asian (SAS) AF: 0.236 AC: 1059 AN: 4482

European-Finnish (FIN) AF: 0.182 AC: 1547 AN: 8488

Middle Eastern (MID) AF: 0.129 AC: 36 AN: 280

European-Non Finnish (NFE) AF: 0.197 AC: 12514 AN: 63458

Other (OTH) AF: 0.190 AC: 375 AN: 1974

Alfa AF: 0.188 Hom.: 4467

Asia WGS AF: 0.365 AC: 1240 AN: 3398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.74
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11533655; hg19: chr12-59942122;