2-65055574-G-C

Variant names:

• chr2-65055574-G-C
• rs6728523
• ENST00000771817.1:n.301C>G

Variant summary

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

The ENST00000771817.1(LINC02245):​n.301C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,052 control chromosomes in the GnomAD database, including 6,492 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 0.29 (6492 hom., cov: 33)
• Consequence: LINC02245 ENST00000771817.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 6 publications found

Genes affected

LINC02245 (HGNC:53134): (long intergenic non-protein coding RNA 2245)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771817.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02245	ENST00000771817.1		n.301C>G		non_coding_transcript_exon	Exon 2 of 4
	LINC02245	ENST00000771818.1		n.338C>G		non_coding_transcript_exon	Exon 2 of 4
	LINC02245	ENST00000771823.1		n.366C>G		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43457 AN: 151934 Hom.: 6470 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43524 AN: 152052 Hom.: 6492 Cov.: 33 AF XY: 0.284 AC XY: 21083 AN XY: 74322

African (AFR) AF: 0.349 AC: 14479 AN: 41444

American (AMR) AF: 0.272 AC: 4152 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1675 AN: 5174

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2237 AN: 10572

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17183 AN: 67972

Other (OTH) AF: 0.310 AC: 654 AN: 2112

Alfa AF: 0.281 Hom.: 775

Bravo AF: 0.293

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.70
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6728523; hg19: chr2-65282708;