rs17546037

Variant names:

• chr5-7217290-A-G
• rs17546037
• ENST00000651243.2:n.491-495A>G

Variant summary

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

The ENST00000651243.2(LINC02196):​n.491-495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,264 control chromosomes in the GnomAD database, including 854 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 (854 hom., cov: 32)
• Consequence: LINC02196 ENST00000651243.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

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=-0.94).
• 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.491-495A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15249 AN: 152146 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.100 AC: 15260 AN: 152264 Hom.: 854 Cov.: 32 AF XY: 0.0992 AC XY: 7383 AN XY: 74442

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.112 Hom.: 171

Bravo AF: 0.0940

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17546037; hg19: chr5-7217403;