rs4695885

Positions:

• chr4-173765195-G-A
• chr4-173765195-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665435.1(LINC02269):​n.64+65998G>A variant causes a intron, non coding transcript 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 ENST00000665435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02269	ENST00000665435.1	n.64+65998G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.304

Alfa AF: 0.327 Hom.: 11024

Bravo AF: 0.290

Asia WGS AF: 0.270 AC: 937 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4695885; hg19: chr4-174686346;