rs7657203

Variant names:

• chr4-173739814-A-G
• rs7657203
• ENST00000654333.1:n.229+4271A>G

Variant summary

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

The ENST00000654333.1(LINC02269):​n.229+4271A>G variant causes a intron 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 ENST00000654333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02269	ENST00000654333.1		n.229+4271A>G		intron	N/A
	LINC02269	ENST00000654653.1		n.229+4271A>G		intron	N/A
	LINC02269	ENST00000654916.1		n.229+4271A>G		intron	N/A

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

African (AFR) AF: 0.0585 AC: 2425 AN: 41430

American (AMR) AF: 0.0310 AC: 472 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0606 AC: 210 AN: 3464

East Asian (EAS) AF: 0.0443 AC: 229 AN: 5164

South Asian (SAS) AF: 0.116 AC: 557 AN: 4798

European-Finnish (FIN) AF: 0.0132 AC: 138 AN: 10460

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1917 AN: 67882

Other (OTH) AF: 0.0447 AC: 94 AN: 2102

Alfa AF: 0.0348 Hom.: 18

Bravo AF: 0.0401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7657203; hg19: chr4-174660965;