3-141689849-A-G

Position:

• chr3-141689849-A-G

Variant summary

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

The NR_136190.1(LINC02618):​n.663-583A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,162 control chromosomes in the GnomAD database, including 65,173 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 0.92 (65173 hom., cov: 30)
• Consequence: LINC02618 NR_136190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

Genes affected

LRRC78P (HGNC:54091): (long intergenic non-protein coding RNA 2618)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02618	NR_136190.1	n.663-583A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC78P	ENST00000474979.4	n.874-583A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000637590.2	n.770-583A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140630 AN: 152044 Hom.: 65113 Cov.: 30

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.925 AC: 140749 AN: 152162 Hom.: 65173 Cov.: 30 AF XY: 0.927 AC XY: 68941 AN XY: 74368

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.923

Alfa AF: 0.903 Hom.: 76199

Bravo AF: 0.928

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6440031; hg19: chr3-141408691;