rs145744974

Variant names:

• chr3-34218600-A-G
• rs145744974
• ENST00000415991.2:n.111+47680A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000415991.2(LINC01811):​n.111+47680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 152,168 control chromosomes in the GnomAD database, including 13 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 0.010 (13 hom., cov: 33)
• Consequence: LINC01811 ENST00000415991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

ENSG00000236452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01811	NR_183676.1	n.156+47680A>G		intron_variant	Intron 2 of 5
LINC01811	NR_183677.1	n.129+47680A>G		intron_variant	Intron 2 of 5
LINC01811	NR_183678.1	n.129+47680A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01811	ENST00000415991.2	n.111+47680A>G		intron_variant	Intron 2 of 5	5
LINC01811	ENST00000424786.5	n.159+47680A>G		intron_variant	Intron 2 of 7	5
ENSG00000236452	ENST00000455974.1	n.65+15292A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0100 AC: 1528 AN: 152050 Hom.: 13 Cov.: 33

Gnomad AFR AF: 0.00258

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00511

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0100 AC: 1529 AN: 152168 Hom.: 13 Cov.: 33 AF XY: 0.0104 AC XY: 774 AN XY: 74398

African (AFR) AF: 0.00258 AC: 107 AN: 41526

American (AMR) AF: 0.00510 AC: 78 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00125 AC: 6 AN: 4810

European-Finnish (FIN) AF: 0.0259 AC: 275 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1025 AN: 67986

Other (OTH) AF: 0.0124 AC: 26 AN: 2104

Alfa AF: 0.0135 Hom.: 2

Bravo AF: 0.00859

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.57
PhyloP100		-0.043
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs145744974; hg19: chr3-34260092;