rs13064954

Variant names:

• chr3-157136953-G-A
• rs13064954
• ENST00000781925.1:n.342-32064G>A

Variant summary

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

The ENST00000781925.1(LINC00881):​n.342-32064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,206 control chromosomes in the GnomAD database, including 614 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 0.078 (614 hom., cov: 32)
• Consequence: LINC00881 ENST00000781925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 21 publications found

Genes affected

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 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
LINC00881	ENST00000781925.1	n.342-32064G>A		intron_variant	Intron 2 of 4
LINC00881	ENST00000781926.1	n.345-21974G>A		intron_variant	Intron 2 of 5
LINC00881	ENST00000781927.1	n.342-32064G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11917 AN: 152088 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0784 AC: 11933 AN: 152206 Hom.: 614 Cov.: 32 AF XY: 0.0798 AC XY: 5940 AN XY: 74420

African (AFR) AF: 0.141 AC: 5847 AN: 41506

American (AMR) AF: 0.0836 AC: 1279 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5182

South Asian (SAS) AF: 0.0824 AC: 397 AN: 4820

European-Finnish (FIN) AF: 0.0763 AC: 809 AN: 10608

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0427 AC: 2901 AN: 68004

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0542 Hom.: 1119

Bravo AF: 0.0836

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs13064954; hg19: chr3-156854742;