18-55085469-C-T

Position:

• chr18-55085469-C-T

Variant summary

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

The XR_935478.3(LINC03035):​n.124G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,968 control chromosomes in the GnomAD database, including 11,891 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 0.39 (11891 hom., cov: 32)
• Consequence: LINC03035 XR_935478.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

Genes affected

LINC03035 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03035	XR_935478.3	n.124G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59794 AN: 151848 Hom.: 11882 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.394 AC: 59833 AN: 151968 Hom.: 11891 Cov.: 32 AF XY: 0.394 AC XY: 29263 AN XY: 74286

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.380

Alfa AF: 0.394 Hom.: 1492

Bravo AF: 0.397

Asia WGS AF: 0.411 AC: 1431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4801131; hg19: chr18-52752700;