rs7620363

Variant names:

• chr3-33971713-C-T
• rs7620363
• ENST00000654751.1:n.716+12188C>T

Variant summary

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

The ENST00000654751.1(LINC01811):​n.716+12188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,196 control chromosomes in the GnomAD database, including 6,496 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 0.26 (6496 hom., cov: 33)
• Consequence: LINC01811 ENST00000654751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654751.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01811	ENST00000654751.1		n.716+12188C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39924 AN: 152080 Hom.: 6500 Cov.: 33

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.262 AC: 39924 AN: 152196 Hom.: 6496 Cov.: 33 AF XY: 0.263 AC XY: 19608 AN XY: 74416

African (AFR) AF: 0.0639 AC: 2654 AN: 41540

American (AMR) AF: 0.317 AC: 4851 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1411 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5174

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10586

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23682 AN: 67990

Other (OTH) AF: 0.305 AC: 644 AN: 2112

Alfa AF: 0.330 Hom.: 6160

Bravo AF: 0.253

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7620363; hg19: chr3-34013205;