rs7654559

Variant names:

• chr4-96389644-T-C
• rs7654559
• ENST00000522173.1:n.64-61848T>C

Variant summary

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

The ENST00000522173.1(LINC02267):​n.64-61848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,116 control chromosomes in the GnomAD database, including 4,295 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 0.23 (4295 hom., cov: 33)
• Consequence: LINC02267 ENST00000522173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 1 publications found

Genes affected

LINC02267 (HGNC:53181): (long intergenic non-protein coding RNA 2267)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522173.1. 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
	LINC02267	NR_147149.1		n.93-61848T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02267	ENST00000522173.1	TSL:3	n.64-61848T>C		intron	N/A
	LINC02267	ENST00000754345.1		n.372+35771T>C		intron	N/A
	LINC02267	ENST00000754346.1		n.267+47948T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35270 AN: 151998 Hom.: 4298 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.232 AC: 35285 AN: 152116 Hom.: 4295 Cov.: 33 AF XY: 0.228 AC XY: 16972 AN XY: 74382

African (AFR) AF: 0.270 AC: 11176 AN: 41466

American (AMR) AF: 0.186 AC: 2839 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3468

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1913 AN: 10600

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16076 AN: 67982

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.240 Hom.: 585

Bravo AF: 0.232

Asia WGS AF: 0.138 AC: 480 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7654559; hg19: chr4-97310795;