ENST00000717721.1:n.316+3513C>G

Variant names:

• chr5-71451743-G-C
• rs7447545
• ENST00000717721.1:n.316+3513C>G

Variant summary

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

The ENST00000717721.1(LINC02197):​n.316+3513C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,954 control chromosomes in the GnomAD database, including 12,090 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 0.38 (12090 hom., cov: 31)
• Consequence: LINC02197 ENST00000717721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717721.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02197	ENST00000717721.1		n.316+3513C>G		intron	N/A
	LINC02197	ENST00000717723.1		n.316+3513C>G		intron	N/A
	LINC02197	ENST00000773728.1		n.38+3813C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58383 AN: 151836 Hom.: 12094 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.384 AC: 58394 AN: 151954 Hom.: 12090 Cov.: 31 AF XY: 0.387 AC XY: 28739 AN XY: 74258

African (AFR) AF: 0.242 AC: 10018 AN: 41458

American (AMR) AF: 0.313 AC: 4781 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1552 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1816 AN: 5156

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4806

European-Finnish (FIN) AF: 0.493 AC: 5205 AN: 10548

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31186 AN: 67930

Other (OTH) AF: 0.402 AC: 847 AN: 2108

Alfa AF: 0.266 Hom.: 673

Bravo AF: 0.361

Asia WGS AF: 0.401 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.43
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7447545; hg19: chr5-70747570;