rs4839516

Variant names:

• chr1-116197828-C-A
• rs4839516
• ENST00000849284.1:n.79-5783C>A

Variant summary

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

The ENST00000849284.1(LINC01779):​n.79-5783C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,140 control chromosomes in the GnomAD database, including 4,065 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 0.20 (4065 hom., cov: 32)
• Consequence: LINC01779 ENST00000849284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 8 publications found

Genes affected

LINC01779 (HGNC:52569): (long intergenic non-protein coding RNA 1779)

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 = 0.289 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
LINC01779	ENST00000849284.1	n.79-5783C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30947 AN: 152022 Hom.: 4062 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.203 AC: 30949 AN: 152140 Hom.: 4065 Cov.: 32 AF XY: 0.198 AC XY: 14724 AN XY: 74374

African (AFR) AF: 0.0620 AC: 2573 AN: 41514

American (AMR) AF: 0.233 AC: 3557 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3468

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5190

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4824

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10572

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19880 AN: 67984

Other (OTH) AF: 0.256 AC: 540 AN: 2108

Alfa AF: 0.246 Hom.: 8806

Bravo AF: 0.199

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.55
DANN	Benign	0.74
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs4839516; hg19: chr1-116740450;