rs986217

Variant names:

• chr5-71448831-A-C
• rs986217
• ENST00000717721.1:n.317-3042T>G

Variant summary

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

The ENST00000717721.1(LINC02197):​n.317-3042T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,032 control chromosomes in the GnomAD database, including 13,371 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 0.41 (13371 hom., cov: 32)
• Consequence: LINC02197 ENST00000717721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 4 publications found

Genes affected

LINC02197 (HGNC:53063): (long intergenic non-protein coding RNA 2197)

ENSG00000249981 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02197	ENST00000717721.1	n.317-3042T>G		intron_variant	Intron 1 of 3
LINC02197	ENST00000717723.1	n.317-3042T>G		intron_variant	Intron 1 of 2
LINC02197	ENST00000773728.1	n.39-3042T>G		intron_variant	Intron 1 of 2
ENSG00000249981	ENST00000774002.1	n.61+3159A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62773 AN: 151914 Hom.: 13373 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.413 AC: 62794 AN: 152032 Hom.: 13371 Cov.: 32 AF XY: 0.414 AC XY: 30787 AN XY: 74328

African (AFR) AF: 0.341 AC: 14147 AN: 41492

American (AMR) AF: 0.326 AC: 4982 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1831 AN: 5170

South Asian (SAS) AF: 0.476 AC: 2298 AN: 4830

European-Finnish (FIN) AF: 0.493 AC: 5208 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31170 AN: 67922

Other (OTH) AF: 0.419 AC: 885 AN: 2112

Alfa AF: 0.427 Hom.: 1325

Bravo AF: 0.393

Asia WGS AF: 0.406 AC: 1414 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs986217; hg19: chr5-70744658;