rs1559033

Variant names:

• chr2-15744432-C-T
• rs1559033
• ENST00000770646.1:n.529-38715C>T

Variant summary

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

The ENST00000770646.1(LINC01804):​n.529-38715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 285,326 control chromosomes in the GnomAD database, including 1,172 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 (1050 hom., cov: 32)
  • Exomes 𝑓: 0.016 (122 hom.)
• Consequence: LINC01804 ENST00000770646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 1 publications found

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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
LINC01804	ENST00000770646.1	n.529-38715C>T		intron_variant	Intron 3 of 4
LINC01804	ENST00000770647.1	n.407-38715C>T		intron_variant	Intron 2 of 3
LINC01804	ENST00000770648.1	n.429+35986C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10509 AN: 151998 Hom.: 1042 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00270

Gnomad FIN AF: 0.00774

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0588

GnomAD4 exome AF: 0.0159 AC: 2117 AN: 133210 Hom.: 122 AF XY: 0.0140 AC XY: 1036 AN XY: 73864

African (AFR) AF: 0.218 AC: 981 AN: 4506

American (AMR) AF: 0.0210 AC: 192 AN: 9148

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 108 AN: 2948

East Asian (EAS) AF: 0.00 AC: 0 AN: 7360

South Asian (SAS) AF: 0.00250 AC: 61 AN: 24406

European-Finnish (FIN) AF: 0.00776 AC: 50 AN: 6440

Middle Eastern (MID) AF: 0.0508 AC: 40 AN: 788

European-Non Finnish (NFE) AF: 0.00780 AC: 555 AN: 71136

Other (OTH) AF: 0.0201 AC: 130 AN: 6478

GnomAD4 genome AF: 0.0693 AC: 10548 AN: 152116 Hom.: 1050 Cov.: 32 AF XY: 0.0675 AC XY: 5019 AN XY: 74368

African (AFR) AF: 0.216 AC: 8948 AN: 41470

American (AMR) AF: 0.0390 AC: 597 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5146

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4814

European-Finnish (FIN) AF: 0.00774 AC: 82 AN: 10600

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00899 AC: 611 AN: 68000

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0486 Hom.: 81

Bravo AF: 0.0775

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.42
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1559033; hg19: chr2-15884556;