rs198175

Positions:

• chr16-24237228-G-A
• chr16-24237228-G-C

Variant summary

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

The NR_146569.1(LINC02194):​n.33+1092G>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 0.665 in 151,860 control chromosomes in the GnomAD database, including 33,867 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 0.67 (33867 hom., cov: 31)
• Consequence: LINC02194 NR_146569.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

LINC02194 (HGNC:53057): (long intergenic non-protein coding RNA 2194)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02194	NR_146569.1	n.33+1092G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02194	ENST00000567127.1	n.33+1092G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100935 AN: 151742 Hom.: 33826 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.665 AC: 101032 AN: 151860 Hom.: 33867 Cov.: 31 AF XY: 0.658 AC XY: 48806 AN XY: 74184

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.633

Alfa AF: 0.632 Hom.: 3103

Bravo AF: 0.669

Asia WGS AF: 0.515 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198175; hg19: chr16-24248549;