rs7657203

chr4-173739814-A-G

Variant summary

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

The ENST00000665435.1(LINC02269):n.64+40617A>G 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 0.04 in 151,714 control chromosomes in the GnomAD database, including 173 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 0.040 (173 hom., cov: 30)
• Consequence: LINC02269 ENST00000665435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02269	ENST00000665435.1	n.64+40617A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6057 AN: 151596 Hom.: 172 Cov.: 30

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0447

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

GnomAD4 genome AF: 0.0400 AC: 6061 AN: 151714 Hom.: 173 Cov.: 30 AF XY: 0.0405 AC XY: 3005 AN XY: 74158

Gnomad4 AFR AF: 0.0585

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0606

Gnomad4 EAS AF: 0.0443

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0447

Alfa AF: 0.0330 Hom.: 11

Bravo AF: 0.0401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.8
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7657203; hg19: chr4-174660965;