rs13155746

Variant names:

• chr5-7218024-G-A
• rs13155746
• ENST00000651243.2:n.730G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-7218024-G-A
• chr5-7218024-G-C
• chr5-7218024-G-T

Variant summary

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

The ENST00000651243.2(LINC02196):​n.730G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,244 control chromosomes in the GnomAD database, including 857 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 (857 hom., cov: 33)
• Consequence: LINC02196 ENST00000651243.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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	ENST00000651243.2	n.730G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15326 AN: 152126 Hom.: 858 Cov.: 33

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.101 AC: 15343 AN: 152244 Hom.: 857 Cov.: 33 AF XY: 0.0998 AC XY: 7426 AN XY: 74424

Gnomad4 AFR AF: 0.0964

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0819

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.103 Hom.: 1095

Bravo AF: 0.0946

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13155746; hg19: chr5-7218137;