rs278357

Variant names:

• chr15-31204844-A-G
• rs278357
• ENST00000685492.1:n.348-1000T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-31204844-A-G
• chr15-31204844-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685492.1(LINC03034):​n.348-1000T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,068 control chromosomes in the GnomAD database, including 26,597 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 0.58 (26597 hom., cov: 32)
• Consequence: LINC03034 ENST00000685492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 3 publications found

Genes affected

LINC03034 (HGNC:54360): (long intergenic non-protein coding RNA 3034)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03034	ENST00000685492.1		n.348-1000T>C		intron	N/A
	LINC03034	ENST00000701141.2		n.355-1000T>C		intron	N/A
	LINC03034	ENST00000701403.2		n.501-1000T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88335 AN: 151950 Hom.: 26546 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.582 AC: 88447 AN: 152068 Hom.: 26597 Cov.: 32 AF XY: 0.583 AC XY: 43343 AN XY: 74338

African (AFR) AF: 0.740 AC: 30697 AN: 41506

American (AMR) AF: 0.541 AC: 8275 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1774 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3724 AN: 5168

South Asian (SAS) AF: 0.543 AC: 2622 AN: 4830

European-Finnish (FIN) AF: 0.548 AC: 5790 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33859 AN: 67938

Other (OTH) AF: 0.549 AC: 1157 AN: 2106

Alfa AF: 0.525 Hom.: 82102

Bravo AF: 0.585

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.86
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs278357; hg19: chr15-31497047;