rs4529739

Variant names:

• chr1-60239111-T-C
• rs4529739
• XR_947430.2:n.150-3714T>C

Variant summary

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

The XR_947430.2(LINC02778):​n.150-3714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,220 control chromosomes in the GnomAD database, including 510 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 0.069 (510 hom., cov: 32)
• Consequence: LINC02778 XR_947430.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 1 publications found

Genes affected

LINC02778 (HGNC:54298): (long intergenic non-protein coding RNA 2778)

LOC105378761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02778	XR_947430.2	n.150-3714T>C		intron_variant	Intron 1 of 4
LOC105378761	XR_947431.2	n.617+12476A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10536 AN: 152102 Hom.: 510 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0692 AC: 10539 AN: 152220 Hom.: 510 Cov.: 32 AF XY: 0.0676 AC XY: 5030 AN XY: 74424

African (AFR) AF: 0.0187 AC: 777 AN: 41568

American (AMR) AF: 0.0580 AC: 886 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0893 AC: 430 AN: 4814

European-Finnish (FIN) AF: 0.0778 AC: 825 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7151 AN: 68002

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0974 Hom.: 644

Bravo AF: 0.0647

Asia WGS AF: 0.0280 AC: 101 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.67
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs4529739; hg19: chr1-60704783;