16-24241601-G-A

Position:

• chr16-24241601-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+5465G>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 0.362 in 151,046 control chromosomes in the GnomAD database, including 11,584 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 0.36 (11584 hom., cov: 28)
• Consequence: LINC02194 NR_146569.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02194	NR_146569.1	n.33+5465G>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+5465G>A		intron_variant, non_coding_transcript_variant		3
LINC02194	ENST00000567624.1	n.52+3568G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54646 AN: 150930 Hom.: 11577 Cov.: 28

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.362 AC: 54682 AN: 151046 Hom.: 11584 Cov.: 28 AF XY: 0.361 AC XY: 26631 AN XY: 73766

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.339

Alfa AF: 0.313 Hom.: 1046

Bravo AF: 0.376

Asia WGS AF: 0.349 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.017
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2021512; hg19: chr16-24252922;