rs2902193

Variant names:

• chr18-55983078-A-G
• rs2902193
• ENST00000589440.1:n.406-34650A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-55983078-A-G
• chr18-55983078-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589440.1(ENSG00000267327):​n.406-34650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,940 control chromosomes in the GnomAD database, including 20,804 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 0.52 (20804 hom., cov: 31)
• Consequence: ENSG00000267327 ENST00000589440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

Genes affected

ENSG00000267327 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

LINC01416 (HGNC:51645): (long intergenic non-protein coding RNA 1416)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 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
ENSG00000267327	ENST00000589440.1	n.406-34650A>G		intron_variant	Intron 1 of 2	2
LINC01416	ENST00000654280.1	n.1512+13630T>C		intron_variant	Intron 1 of 3
LINC01416	ENST00000655696.1	n.1303+13630T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78519 AN: 151822 Hom.: 20761 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.517 AC: 78627 AN: 151940 Hom.: 20804 Cov.: 31 AF XY: 0.521 AC XY: 38658 AN XY: 74214

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.538

Alfa AF: 0.546 Hom.: 43874

Bravo AF: 0.507

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902193; hg19: chr18-53650309;