16-24238522-G-A

Variant names:

• chr16-24238522-G-A
• rs392728
• ENST00000567127.1:n.33+2386G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567127.1(LINC02194):​n.33+2386G>A variant causes a intron 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 ENST00000567127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02194	NR_146569.1	n.33+2386G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02194	ENST00000567127.1	n.33+2386G>A		intron_variant	Intron 1 of 3	3
LINC02194	ENST00000567624.1	n.52+489G>A		intron_variant	Intron 1 of 1	3
LINC02194	ENST00000747929.1	n.236+470G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.668 AC: 27728 AN: 41486

American (AMR) AF: 0.661 AC: 10100 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2445 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2147 AN: 5166

South Asian (SAS) AF: 0.720 AC: 3472 AN: 4824

European-Finnish (FIN) AF: 0.527 AC: 5554 AN: 10542

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47535 AN: 67976

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.692 Hom.: 4728

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs392728; hg19: chr16-24249843;