rs2646965

Positions:

• chr18-56025735-C-A
• chr18-56025735-C-T

Variant summary

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

The XR_001753454.2(LINC03092):​n.4833C>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 0.535 in 151,868 control chromosomes in the GnomAD database, including 22,705 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 (22705 hom., cov: 32)
• Consequence: LINC03092 XR_001753454.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

Genes affected

LINC03092 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03092	XR_001753454.2	n.4833C>A		non_coding_transcript_exon_variant	2/2
LINC03069	NR_148972.1	n.2212-340G>T		intron_variant, non_coding_transcript_variant
LINC03092	XR_001753453.3	n.2454C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03069	ENST00000382897.2	n.2212-340G>T		intron_variant, non_coding_transcript_variant		2
LINC03092	ENST00000666716.1	n.2714C>A		non_coding_transcript_exon_variant	2/2
LINC03069	ENST00000650203.1	n.1463-340G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81226 AN: 151750 Hom.: 22673 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.535 AC: 81313 AN: 151868 Hom.: 22705 Cov.: 32 AF XY: 0.533 AC XY: 39534 AN XY: 74200

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.523

Alfa AF: 0.513 Hom.: 3469

Bravo AF: 0.554

Asia WGS AF: 0.495 AC: 1716 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	11
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2646965; hg19: chr18-53692966;