rs6896438

Variant names:

• chr5-159120868-C-G
• rs6896438
• ENST00000826187.1:n.207+20030C>G

Variant summary

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

The ENST00000826187.1(LINC02202):​n.207+20030C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,038 control chromosomes in the GnomAD database, including 24,326 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 0.54 (24326 hom., cov: 32)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 4 publications found

Genes affected

LINC02202 (HGNC:53068): (long intergenic non-protein coding RNA 2202)

ENSG00000307478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000826187.1	n.207+20030C>G		intron_variant	Intron 1 of 2
LINC02202	ENST00000826188.1	n.161+20030C>G		intron_variant	Intron 1 of 1
LINC02202	ENST00000826189.1	n.57+130C>G		intron_variant	Intron 1 of 3
ENSG00000307478	ENST00000826484.1	n.113-8748G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82755 AN: 151920 Hom.: 24308 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.545 AC: 82818 AN: 152038 Hom.: 24326 Cov.: 32 AF XY: 0.556 AC XY: 41275 AN XY: 74300

African (AFR) AF: 0.338 AC: 13983 AN: 41424

American (AMR) AF: 0.644 AC: 9824 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3470

East Asian (EAS) AF: 0.951 AC: 4929 AN: 5182

South Asian (SAS) AF: 0.820 AC: 3958 AN: 4824

European-Finnish (FIN) AF: 0.592 AC: 6262 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40111 AN: 67980

Other (OTH) AF: 0.551 AC: 1163 AN: 2110

Alfa AF: 0.542 Hom.: 2810

Bravo AF: 0.536

Asia WGS AF: 0.820 AC: 2850 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	1.5
DANN	Benign	0.22
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6896438; hg19: chr5-158547876; COSMIC: COSV72296801;