chr5-8328670-G-T

Variant names:

• chr5-8328670-G-T
• rs925203
• ENST00000654773.1:n.261+37507C>A

Variant summary

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

The ENST00000654773.1(LINC02226):​n.261+37507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,652 control chromosomes in the GnomAD database, including 4,671 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 (4671 hom., cov: 31)
• Consequence: LINC02226 ENST00000654773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 3 publications found

Genes affected

LINC02226 (HGNC:53095): (long intergenic non-protein coding RNA 2226)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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
LINC02226	ENST00000654773.1	n.261+37507C>A		intron_variant	Intron 1 of 1
LINC02226	ENST00000847314.1	n.357+58857C>A		intron_variant	Intron 3 of 4
LINC02226	ENST00000847315.1	n.358+58857C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36056 AN: 151536 Hom.: 4662 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.238 AC: 36098 AN: 151652 Hom.: 4671 Cov.: 31 AF XY: 0.242 AC XY: 17930 AN XY: 74102

African (AFR) AF: 0.234 AC: 9660 AN: 41298

American (AMR) AF: 0.297 AC: 4529 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2410 AN: 5142

South Asian (SAS) AF: 0.424 AC: 2038 AN: 4802

European-Finnish (FIN) AF: 0.171 AC: 1794 AN: 10476

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13967 AN: 67932

Other (OTH) AF: 0.270 AC: 569 AN: 2106

Alfa AF: 0.222 Hom.: 16662

Bravo AF: 0.245

Asia WGS AF: 0.429 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.32
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs925203; hg19: chr5-8328783;