4-173765195-G-A

Variant names:

• chr4-173765195-G-A
• rs4695885
• ENST00000654333.1:n.229+29652G>A

Variant summary

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

The ENST00000654333.1(LINC02269):​n.229+29652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,084 control chromosomes in the GnomAD database, including 6,730 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 0.28 (6730 hom., cov: 33)
• Consequence: LINC02269 ENST00000654333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

Genes affected

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

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 (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654333.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02269	ENST00000654333.1		n.229+29652G>A		intron	N/A
	LINC02269	ENST00000654653.1		n.229+29652G>A		intron	N/A
	LINC02269	ENST00000654916.1		n.229+29652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42646 AN: 151966 Hom.: 6725 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.280 AC: 42651 AN: 152084 Hom.: 6730 Cov.: 33 AF XY: 0.278 AC XY: 20627 AN XY: 74324

African (AFR) AF: 0.135 AC: 5604 AN: 41516

American (AMR) AF: 0.397 AC: 6055 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1697 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2804 AN: 10566

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23367 AN: 67958

Other (OTH) AF: 0.304 AC: 641 AN: 2110

Alfa AF: 0.327 Hom.: 13181

Bravo AF: 0.290

Asia WGS AF: 0.270 AC: 937 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4695885; hg19: chr4-174686346;