3-127552477-G-A

Variant names:

• chr3-127552477-G-A
• rs10049478
• ENST00000804549.1:n.111-2424G>A

Variant summary

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

The ENST00000804549.1(ENSG00000304561):​n.111-2424G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,200 control chromosomes in the GnomAD database, including 2,960 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 0.17 (2960 hom., cov: 33)
• Consequence: ENSG00000304561 ENST00000804549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 publications found

Genes affected

ENSG00000304561 (HGNC:):

LINC02034 (HGNC:52868): (long intergenic non-protein coding RNA 2034)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804549.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304561	ENST00000804549.1		n.111-2424G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25730 AN: 152082 Hom.: 2960 Cov.: 33

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.169 AC: 25729 AN: 152200 Hom.: 2960 Cov.: 33 AF XY: 0.173 AC XY: 12853 AN XY: 74400

African (AFR) AF: 0.0406 AC: 1688 AN: 41544

American (AMR) AF: 0.118 AC: 1810 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3472

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5190

South Asian (SAS) AF: 0.167 AC: 808 AN: 4828

European-Finnish (FIN) AF: 0.339 AC: 3583 AN: 10576

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16219 AN: 67988

Other (OTH) AF: 0.172 AC: 363 AN: 2112

Alfa AF: 0.220 Hom.: 2109

Bravo AF: 0.146

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.058
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10049478; hg19: chr3-127271320;