rs17546037

Positions:

• chr5-7217290-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02196	ENST00000651243.2	n.491-495A>G		intron_variant, non_coding_transcript_variant

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;