rs17192980

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512838.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02196	ENST00000512838.2	TSL:4	n.69+43917T>C		intron	N/A
	LINC02196	ENST00000648809.1		n.362+53727T>C		intron	N/A
	LINC02196	ENST00000715905.1		n.277+53727T>C		intron	N/A

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

African (AFR) AF: 0.0778 AC: 3234 AN: 41556

American (AMR) AF: 0.150 AC: 2288 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3472

East Asian (EAS) AF: 0.0976 AC: 505 AN: 5174

South Asian (SAS) AF: 0.151 AC: 731 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1550 AN: 10600

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6898 AN: 68022

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.105 Hom.: 1474

Bravo AF: 0.106

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17192980;

hg19: chr5-6977768;