rs6556398

Variant names:

• chr5-159146229-A-C
• rs6556398
• ENST00000826187.1:n.208-15120A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-159146229-A-C
• chr5-159146229-A-G

Variant summary

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

The ENST00000826187.1(LINC02202):​n.208-15120A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,056 control chromosomes in the GnomAD database, including 45,234 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 0.76 (45234 hom., cov: 31)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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.208-15120A>C		intron_variant	Intron 1 of 2
LINC02202	ENST00000826188.1	n.162-15120A>C		intron_variant	Intron 1 of 1
LINC02202	ENST00000826189.1	n.110+10046A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115998 AN: 151938 Hom.: 45181 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.764 AC: 116110 AN: 152056 Hom.: 45234 Cov.: 31 AF XY: 0.762 AC XY: 56653 AN XY: 74304

African (AFR) AF: 0.932 AC: 38681 AN: 41496

American (AMR) AF: 0.751 AC: 11475 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2516 AN: 3468

East Asian (EAS) AF: 0.569 AC: 2931 AN: 5154

South Asian (SAS) AF: 0.786 AC: 3785 AN: 4816

European-Finnish (FIN) AF: 0.675 AC: 7118 AN: 10544

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 47036 AN: 67986

Other (OTH) AF: 0.775 AC: 1637 AN: 2112

Alfa AF: 0.746 Hom.: 5549

Bravo AF: 0.770

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6556398; hg19: chr5-158573237; COSMIC: COSV60222524;