12-73207352-C-T

Variant names:

• chr12-73207352-C-T
• rs11615274
• ENST00000550723.1:n.386-95C>T

Variant summary

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

The ENST00000550723.1(LINC02444):​n.386-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,912 control chromosomes in the GnomAD database, including 3,475 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 0.20 (3474 hom., cov: 31)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: LINC02444 ENST00000550723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 10 publications found

Genes affected

LINC02444 (HGNC:53376): (long intergenic non-protein coding RNA 2444)

ENSG00000258294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550723.1. 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
	LINC02444	NR_110130.1		n.386-95C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02444	ENST00000550723.1	TSL:1	n.386-95C>T		intron	N/A
	ENSG00000258294	ENST00000551934.2	TSL:2	n.142+25309G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30509 AN: 151776 Hom.: 3473 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.333 AC: 6 AN: 18 Hom.: 1 AF XY: 0.286 AC XY: 4 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.429 AC: 6 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.201 AC: 30511 AN: 151894 Hom.: 3474 Cov.: 31 AF XY: 0.201 AC XY: 14886 AN XY: 74238

African (AFR) AF: 0.100 AC: 4162 AN: 41480

American (AMR) AF: 0.160 AC: 2433 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3466

East Asian (EAS) AF: 0.113 AC: 581 AN: 5142

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10556

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17812 AN: 67894

Other (OTH) AF: 0.204 AC: 430 AN: 2108

Alfa AF: 0.240 Hom.: 20420

Bravo AF: 0.187

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11615274; hg19: chr12-73601132;