2-228566205-T-C

Variant names:

• chr2-228566205-T-C
• rs1435850
• ENST00000432481.2:n.144+45047A>G

Variant summary

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

The ENST00000432481.2(LINC01807):​n.144+45047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,768 control chromosomes in the GnomAD database, including 33,671 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 0.65 (33671 hom., cov: 30)
• Consequence: LINC01807 ENST00000432481.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 7 publications found

Genes affected

LINC01807 (HGNC:52610): (long intergenic non-protein coding RNA 1807)

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 (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01807	NR_151716.1	n.144+45047A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01807	ENST00000432481.2	n.144+45047A>G		intron_variant	Intron 1 of 3	3
LINC01807	ENST00000656071.1	n.313+2049A>G		intron_variant	Intron 1 of 2
LINC01807	ENST00000665053.1	n.126-77412A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98129 AN: 151650 Hom.: 33655 Cov.: 30

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.647 AC: 98165 AN: 151768 Hom.: 33671 Cov.: 30 AF XY: 0.655 AC XY: 48556 AN XY: 74176

African (AFR) AF: 0.402 AC: 16615 AN: 41322

American (AMR) AF: 0.780 AC: 11890 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3470

East Asian (EAS) AF: 0.925 AC: 4744 AN: 5128

South Asian (SAS) AF: 0.850 AC: 4087 AN: 4808

European-Finnish (FIN) AF: 0.696 AC: 7340 AN: 10542

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48816 AN: 67946

Other (OTH) AF: 0.700 AC: 1470 AN: 2100

Alfa AF: 0.708 Hom.: 21109

Bravo AF: 0.639

Asia WGS AF: 0.848 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1435850; hg19: chr2-229430921;