5-17437385-A-G

Position:

• chr5-17437385-A-G

Variant summary

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

The NR_134275.1(LINC02217):​n.71-4084A>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 0.65 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 NR_134275.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02217	NR_134275.1	n.71-4084A>G		intron_variant, non_coding_transcript_variant
LINC02217	NR_134273.1	n.477+172A>G		intron_variant, non_coding_transcript_variant
LINC02217	NR_134274.1	n.207-4084A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02217	ENST00000652939.1	n.129-4084A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.710

Alfa AF: 0.799 Hom.: 78297

Bravo AF: 0.625

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs871722; hg19: chr5-17437494;