3-34520578-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC01811	ENST00000424786.5	n.571-36010A>T		intron_variant	Intron 6 of 7	5
LINC01811	ENST00000655650.1	n.310-30829A>T		intron_variant	Intron 3 of 6
LINC01811	ENST00000656055.1	n.542-30824A>T		intron_variant	Intron 5 of 9

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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.691

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.26
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

Publications

LitVar

Other links and lift over

dbSNP: rs2122231; hg19: chr3-34562070;