rs12629106

Variant names:

• chr3-177377284-C-T
• rs12629106
• ENST00000850243.1:n.78C>T

Variant summary

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

The ENST00000850243.1(LINC00578):​n.78C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,868 control chromosomes in the GnomAD database, including 1,785 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 0.15 (1785 hom., cov: 32)
• Consequence: LINC00578 ENST00000850243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 10 publications found

Genes affected

LINC00578 (HGNC:43807): (long intergenic non-protein coding RNA 578)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 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
LINC00578	ENST00000850243.1	n.78C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22553 AN: 151750 Hom.: 1780 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.149 AC: 22576 AN: 151868 Hom.: 1785 Cov.: 32 AF XY: 0.148 AC XY: 11012 AN XY: 74216

African (AFR) AF: 0.135 AC: 5586 AN: 41362

American (AMR) AF: 0.120 AC: 1837 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.183 AC: 945 AN: 5172

South Asian (SAS) AF: 0.0939 AC: 451 AN: 4802

European-Finnish (FIN) AF: 0.187 AC: 1976 AN: 10552

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11079 AN: 67950

Other (OTH) AF: 0.132 AC: 277 AN: 2104

Alfa AF: 0.158 Hom.: 8911

Bravo AF: 0.146

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.2
DANN	Benign	0.80
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12629106; hg19: chr3-177095072;