rs7620363

Positions:

• chr3-33971713-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654751.1(LINC01811):​n.716+12188C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01811	ENST00000654751.1	n.716+12188C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.305

Alfa AF: 0.337 Hom.: 4334

Bravo AF: 0.253

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7620363; hg19: chr3-34013205;