chr3-34520578-A-T

Variant names:

• chr3-34520578-A-T
• rs2122231
• ENST00000424786.5:n.571-36010A>T

Variant summary

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

The ENST00000424786.5(LINC01811):​n.571-36010A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 151,890 control chromosomes in the GnomAD database, including 37,505 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 0.70 (37505 hom., cov: 32)
• Consequence: LINC01811 ENST00000424786.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424786.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01811	ENST00000424786.5	TSL:5	n.571-36010A>T		intron	N/A
	LINC01811	ENST00000655650.1		n.310-30829A>T		intron	N/A
	LINC01811	ENST00000656055.1		n.542-30824A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105464 AN: 151770 Hom.: 37461 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.695 AC: 105567 AN: 151890 Hom.: 37505 Cov.: 32 AF XY: 0.702 AC XY: 52095 AN XY: 74232

African (AFR) AF: 0.802 AC: 33249 AN: 41472

American (AMR) AF: 0.660 AC: 10068 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1897 AN: 3468

East Asian (EAS) AF: 0.990 AC: 5119 AN: 5170

South Asian (SAS) AF: 0.784 AC: 3771 AN: 4810

European-Finnish (FIN) AF: 0.706 AC: 7446 AN: 10544

Middle Eastern (MID) AF: 0.676 AC: 196 AN: 290

European-Non Finnish (NFE) AF: 0.614 AC: 41630 AN: 67852

Other (OTH) AF: 0.691 AC: 1459 AN: 2112

Alfa AF: 0.651 Hom.: 4057

Bravo AF: 0.698

Asia WGS AF: 0.870 AC: 3024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.26
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs2122231; hg19: chr3-34562070;