5-17437385-A-G

Variant names:

• chr5-17437385-A-G
• rs871722
• ENST00000505844.2:n.477+172A>G

Variant summary

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

The ENST00000505844.2(LINC02217):​n.477+172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,170 control chromosomes in the GnomAD database, including 37,383 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 0.65 (37383 hom., cov: 33)
• Consequence: LINC02217 ENST00000505844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 7 publications found

Genes affected

LINC02217 (HGNC:53084): (long intergenic non-protein coding RNA 2217)

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 (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505844.2. 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
	LINC02217	NR_134273.1		n.477+172A>G		intron	N/A
	LINC02217	NR_134274.1		n.207-4084A>G		intron	N/A
	LINC02217	NR_134275.1		n.71-4084A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02217	ENST00000505844.2	TSL:2	n.477+172A>G		intron	N/A
	LINC02217	ENST00000507730.6	TSL:3	n.339-4084A>G		intron	N/A
	LINC02217	ENST00000508677.1	TSL:3	n.71-4084A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98950 AN: 152052 Hom.: 37377 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.650 AC: 98967 AN: 152170 Hom.: 37383 Cov.: 33 AF XY: 0.655 AC XY: 48774 AN XY: 74418

African (AFR) AF: 0.235 AC: 9731 AN: 41468

American (AMR) AF: 0.713 AC: 10898 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2899 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4707 AN: 5180

South Asian (SAS) AF: 0.757 AC: 3656 AN: 4830

European-Finnish (FIN) AF: 0.837 AC: 8881 AN: 10606

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55623 AN: 68008

Other (OTH) AF: 0.710 AC: 1499 AN: 2112

Alfa AF: 0.768 Hom.: 110103

Bravo AF: 0.625

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs871722; hg19: chr5-17437494;