5-44627903-C-T

Variant names:

• chr5-44627903-C-T
• rs12652273
• ENST00000671607.1:n.108+30559G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671607.1(LINC02224):​n.108+30559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,490 control chromosomes in the GnomAD database, including 2,958 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 0.18 (2958 hom., cov: 32)
• Consequence: LINC02224 ENST00000671607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

LINC02224 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
LINC02224	ENST00000671607.1	n.108+30559G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27124 AN: 151372 Hom.: 2951 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.179 AC: 27154 AN: 151490 Hom.: 2958 Cov.: 32 AF XY: 0.178 AC XY: 13183 AN XY: 74042

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.163

Alfa AF: 0.0709 Hom.: 82

Bravo AF: 0.189

Asia WGS AF: 0.134 AC: 463 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12652273; hg19: chr5-44628005;