rs773217

Variant names:

• chr3-106851307-T-A
• rs773217
• ENST00000484698.5:n.629-11715A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-106851307-T-A
• chr3-106851307-T-C
• chr3-106851307-T-G

Variant summary

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

The ENST00000484698.5(LINC00882):​n.629-11715A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 152,244 control chromosomes in the GnomAD database, including 75,187 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 0.99 (75187 hom., cov: 31)
• Consequence: LINC00882 ENST00000484698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 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
LINC00882	ENST00000484698.5	n.629-11715A>T		intron_variant	Intron 6 of 7	1
LINC00882	ENST00000655451.1	n.730-8051A>T		intron_variant	Intron 7 of 8
LINC00882	ENST00000656342.1	n.966-11715A>T		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.994 AC: 151194 AN: 152126 Hom.: 75138 Cov.: 31

Gnomad AFR AF: 0.979

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.995

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

GnomAD4 genome AF: 0.994 AC: 151302 AN: 152244 Hom.: 75187 Cov.: 31 AF XY: 0.994 AC XY: 73993 AN XY: 74444

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.997

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.995

Alfa AF: 0.997 Hom.: 9213

Bravo AF: 0.993

Asia WGS AF: 0.997 AC: 3467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.092
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs773217; hg19: chr3-106570154;