ENST00000512838.2:n.155-52381G>A

Variant names:

• chr5-7096387-G-A
• rs7702920
• ENST00000512838.2:n.155-52381G>A

Variant summary

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

The ENST00000512838.2(LINC02196):​n.155-52381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,708 control chromosomes in the GnomAD database, including 2,304 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 0.15 (2304 hom., cov: 32)
• Consequence: LINC02196 ENST00000512838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 1 publications found

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

ENSG00000308577 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02196	XR_001742592.2	n.86-52381G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02196	ENST00000512838.2	n.155-52381G>A		intron_variant	Intron 2 of 6	4
LINC02196	ENST00000648809.1	n.448-52381G>A		intron_variant	Intron 3 of 5
LINC02196	ENST00000651243.2	n.108-52381G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22632 AN: 151590 Hom.: 2297 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.149 AC: 22649 AN: 151708 Hom.: 2304 Cov.: 32 AF XY: 0.153 AC XY: 11359 AN XY: 74168

African (AFR) AF: 0.202 AC: 8356 AN: 41294

American (AMR) AF: 0.237 AC: 3614 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5152

South Asian (SAS) AF: 0.278 AC: 1332 AN: 4796

European-Finnish (FIN) AF: 0.0979 AC: 1032 AN: 10538

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0840 AC: 5703 AN: 67896

Other (OTH) AF: 0.144 AC: 303 AN: 2106

Alfa AF: 0.112 Hom.: 166

Bravo AF: 0.162

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.049
DANN	Benign	0.25
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7702920; hg19: chr5-7096500;