chr5-158391732-C-A

Variant names:

• chr5-158391732-C-A
• rs74620148
• ENST00000619068.1:n.128+17914G>T

Variant summary

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

The ENST00000619068.1(LINC02227):​n.128+17914G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 151,848 control chromosomes in the GnomAD database, including 395 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 0.043 (395 hom., cov: 32)
• Consequence: LINC02227 ENST00000619068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 2 publications found

Genes affected

LINC02227 (HGNC:53096): (long intergenic non-protein coding RNA 2227)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02227	NR_109888.1	n.128+17914G>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02227	ENST00000619068.1	n.128+17914G>T		intron_variant	Intron 1 of 6	1
LINC02227	ENST00000809484.1	n.274+1405G>T		intron_variant	Intron 3 of 3
LINC02227	ENST00000809485.1	n.214-22122G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6564 AN: 151730 Hom.: 390 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00936

Gnomad FIN AF: 0.000662

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0434 AC: 6591 AN: 151848 Hom.: 395 Cov.: 32 AF XY: 0.0418 AC XY: 3106 AN XY: 74220

African (AFR) AF: 0.130 AC: 5389 AN: 41410

American (AMR) AF: 0.0170 AC: 259 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3468

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5150

South Asian (SAS) AF: 0.00916 AC: 44 AN: 4804

European-Finnish (FIN) AF: 0.000662 AC: 7 AN: 10570

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 736 AN: 67890

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0206 Hom.: 36

Bravo AF: 0.0483

Asia WGS AF: 0.0180 AC: 63 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
DANN	Benign	0.32
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs74620148; hg19: chr5-157818740;