chr3-117855975-A-C

Position:

• chr3-117855975-A-C

Variant summary

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

The ENST00000484092.1(LINC03051):​n.411+141207T>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 0.436 in 151,932 control chromosomes in the GnomAD database, including 15,545 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 0.44 (15545 hom., cov: 32)
• Consequence: LINC03051 ENST00000484092.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

LINC03051 (HGNC:56330): (long intergenic non-protein coding RNA 3051)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03051	ENST00000484092.1	n.411+141207T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66282 AN: 151812 Hom.: 15545 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 66306 AN: 151932 Hom.: 15545 Cov.: 32 AF XY: 0.442 AC XY: 32860 AN XY: 74284

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.430

Alfa AF: 0.483 Hom.: 14522

Bravo AF: 0.418

Asia WGS AF: 0.484 AC: 1675 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6438424; hg19: chr3-117574822;