16-24237228-G-A

Variant names:

• chr16-24237228-G-A
• rs198175
• ENST00000567127.1:n.33+1092G>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+1092G>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 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 ENST00000567127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02194	NR_146569.1		n.33+1092G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02194	ENST00000567127.1	TSL:3	n.33+1092G>A		intron	N/A
	LINC02194	ENST00000747929.1		n.65-653G>A		intron	N/A

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

African (AFR) AF: 0.669 AC: 27728 AN: 41426

American (AMR) AF: 0.661 AC: 10102 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2446 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2144 AN: 5138

South Asian (SAS) AF: 0.719 AC: 3462 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5525 AN: 10476

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47522 AN: 67946

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.634 Hom.: 3279

Bravo AF: 0.669

Asia WGS AF: 0.515 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.85
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs198175; hg19: chr16-24248549;