5-158377449-C-T

Variant names:

• chr5-158377449-C-T
• rs9313772
• ENST00000619068.1:n.129-7839G>A

Variant summary

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

The ENST00000619068.1(LINC02227):​n.129-7839G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,980 control chromosomes in the GnomAD database, including 7,553 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 0.30 (7553 hom., cov: 32)
• Consequence: LINC02227 ENST00000619068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 28 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02227	NR_109888.1		n.129-7839G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02227	ENST00000619068.1	TSL:1	n.129-7839G>A		intron	N/A
	LINC02227	ENST00000809484.1		n.275-7839G>A		intron	N/A
	LINC02227	ENST00000809485.1		n.214-7839G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46208 AN: 151862 Hom.: 7552 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.304 AC: 46222 AN: 151980 Hom.: 7553 Cov.: 32 AF XY: 0.303 AC XY: 22541 AN XY: 74282

African (AFR) AF: 0.193 AC: 8010 AN: 41460

American (AMR) AF: 0.340 AC: 5192 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3468

East Asian (EAS) AF: 0.140 AC: 727 AN: 5182

South Asian (SAS) AF: 0.373 AC: 1794 AN: 4810

European-Finnish (FIN) AF: 0.333 AC: 3509 AN: 10552

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24484 AN: 67936

Other (OTH) AF: 0.341 AC: 721 AN: 2114

Alfa AF: 0.342 Hom.: 30642

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9313772;

hg19: chr5-157804457;