rs13155334

chr5-7189411-C-A

Variant summary

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

The ENST00000512838.2(LINC02196):n.538-1371C>A 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 0.128 in 151,884 control chromosomes in the GnomAD database, including 1,648 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 0.13 (1648 hom., cov: 33)
• Consequence: LINC02196 ENST00000512838.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02196	ENST00000512838.2	n.538-1371C>A		intron_variant, non_coding_transcript_variant		4
LINC02196	ENST00000651243.2	n.490+10309C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19479 AN: 151766 Hom.: 1645 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.128 AC: 19509 AN: 151884 Hom.: 1648 Cov.: 33 AF XY: 0.127 AC XY: 9398 AN XY: 74206

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0353

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.117

Alfa AF: 0.114 Hom.: 1584

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13155334; hg19: chr5-7189524;