rs392728

Positions:

• chr16-24238522-G-A

Variant summary

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

The NR_146569.1(LINC02194):​n.33+2386G>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 152,050 control chromosomes in the GnomAD database, including 33,880 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 0.66 (33880 hom., cov: 32)
• Consequence: LINC02194 NR_146569.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02194	NR_146569.1	n.33+2386G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02194	ENST00000567127.1	n.33+2386G>A		intron_variant, non_coding_transcript_variant		3
LINC02194	ENST00000567624.1	n.52+489G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100992 AN: 151932 Hom.: 33840 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.649

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: 101088 AN: 152050 Hom.: 33880 Cov.: 32 AF XY: 0.657 AC XY: 48837 AN XY: 74286

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.634

Alfa AF: 0.693 Hom.: 4553

Bravo AF: 0.669

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs392728; hg19: chr16-24249843;