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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03034	ENST00000685492.1	n.348-1000T>C		intron_variant	Intron 3 of 4
LINC03034	ENST00000701141.1	n.313-1000T>C		intron_variant	Intron 2 of 3
LINC03034	ENST00000701403.1	n.499-1000T>C		intron_variant	Intron 3 of 4

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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.549

Alfa AF: 0.514 Hom.: 33483

Bravo AF: 0.585

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs278357; hg19: chr15-31497047;