1-220485547-C-T

Variant names:

• chr1-220485547-C-T
• rs3842967
• ENST00000446169.3:n.501-107G>A

Variant summary

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

The ENST00000446169.3(LINC02779):​n.501-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,134 control chromosomes in the GnomAD database, including 36,783 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 0.68 (36779 hom., cov: 33)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: LINC02779 ENST00000446169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 4 publications found

Genes affected

LINC02779 (HGNC:54299): (long intergenic non-protein coding RNA 2779)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446169.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02779	NR_185879.1		n.478-107G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02779	ENST00000446169.3	TSL:3	n.501-107G>A		intron	N/A
	LINC02779	ENST00000785452.1		n.559+1444G>A		intron	N/A
	LINC02779	ENST00000785453.1		n.255+1728G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103290 AN: 152010 Hom.: 36781 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.698

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.679 AC: 103318 AN: 152126 Hom.: 36779 Cov.: 33 AF XY: 0.682 AC XY: 50682 AN XY: 74368

African (AFR) AF: 0.467 AC: 19376 AN: 41490

American (AMR) AF: 0.701 AC: 10702 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2507 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2730 AN: 5170

South Asian (SAS) AF: 0.729 AC: 3516 AN: 4820

European-Finnish (FIN) AF: 0.827 AC: 8759 AN: 10586

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53269 AN: 67996

Other (OTH) AF: 0.699 AC: 1477 AN: 2114

Alfa AF: 0.739 Hom.: 131944

Bravo AF: 0.654

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.58

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3842967;

hg19: chr1-220658889;