chr5-44515833-A-C

Variant names:

• chr5-44515833-A-C
• rs13153459
• ENST00000671607.1:n.109-11361T>G

Variant summary

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

The ENST00000671607.1(LINC02224):​n.109-11361T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,790 control chromosomes in the GnomAD database, including 4,799 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 0.24 (4799 hom., cov: 31)
• Consequence: LINC02224 ENST00000671607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

Genes affected

LINC02224 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02224	ENST00000671607.1	n.109-11361T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36003 AN: 151672 Hom.: 4786 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.237 AC: 36035 AN: 151790 Hom.: 4799 Cov.: 31 AF XY: 0.236 AC XY: 17536 AN XY: 74182

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.228

Alfa AF: 0.189 Hom.: 2123

Bravo AF: 0.247

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13153459; hg19: chr5-44515935;