rs4687991

chr3-117746384-G-Achr3-117746384-G-C

Variant summary

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

The ENST00000484092.1(LINC03051):n.412-74088C>T 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 0.539 in 151,904 control chromosomes in the GnomAD database, including 23,505 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 (23505 hom., cov: 32)
• Consequence: LINC03051 ENST00000484092.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101926953	XR_007096020.1	n.514+3273G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03051	ENST00000484092.1	n.412-74088C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000656192.1	n.517+3273G>A		intron_variant, non_coding_transcript_variant
	ENST00000655238.1	n.496+3273G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81773 AN: 151786 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.539 AC: 81801 AN: 151904 Hom.: 23505 Cov.: 32 AF XY: 0.538 AC XY: 39887 AN XY: 74204

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.587

Alfa AF: 0.608 Hom.: 15044

Bravo AF: 0.540

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.21
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4687991; hg19: chr3-117465231;