rs17192980

Variant names:

• chr5-6977655-T-C
• rs17192980
• ENST00000512838.2:n.69+43917T>C

Variant summary

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

The ENST00000512838.2(LINC02196):​n.69+43917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,262 control chromosomes in the GnomAD database, including 969 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 0.10 (969 hom., cov: 33)
• Consequence: LINC02196 ENST00000512838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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
LINC02196	ENST00000512838.2	n.69+43917T>C		intron_variant	Intron 1 of 6	4
LINC02196	ENST00000648809.1	n.362+53727T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15949 AN: 152144 Hom.: 968 Cov.: 33

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0976

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.105 AC: 15970 AN: 152262 Hom.: 969 Cov.: 33 AF XY: 0.108 AC XY: 8022 AN XY: 74458

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.109

Alfa AF: 0.105 Hom.: 1185

Bravo AF: 0.106

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
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: rs17192980; hg19: chr5-6977768;