chr18-56179136-G-C

Variant names:

• chr18-56179136-G-C
• rs1792737
• ENST00000382897.2:n.698+2213C>G

Variant summary

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

The ENST00000382897.2(LINC01539):​n.698+2213C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,034 control chromosomes in the GnomAD database, including 9,866 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 0.34 (9866 hom., cov: 32)
• Consequence: LINC01539 ENST00000382897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 5 publications found

Genes affected

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03069	NR_148972.1	n.698+2213C>G		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01539	ENST00000382897.2	n.698+2213C>G		intron_variant	Intron 3 of 8	2
LINC01539	ENST00000715823.1	n.383+2213C>G		intron_variant	Intron 2 of 3
LINC01539	ENST00000765110.1	n.283+2213C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51006 AN: 151916 Hom.: 9864 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.336 AC: 51008 AN: 152034 Hom.: 9866 Cov.: 32 AF XY: 0.343 AC XY: 25504 AN XY: 74280

African (AFR) AF: 0.179 AC: 7418 AN: 41500

American (AMR) AF: 0.390 AC: 5956 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4197 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4808

European-Finnish (FIN) AF: 0.408 AC: 4300 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24780 AN: 67956

Other (OTH) AF: 0.334 AC: 705 AN: 2108

Alfa AF: 0.352 Hom.: 1218

Bravo AF: 0.329

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.65
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1792737; hg19: chr18-53846367;