rs1316386

chr3-72127374-T-A

Variant summary

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

The ENST00000626474.3(LINC00877):n.456-27364A>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 0.318 in 152,018 control chromosomes in the GnomAD database, including 7,832 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 0.32 (7832 hom., cov: 32)
• Consequence: LINC00877 ENST00000626474.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.80

Genes affected

LINC00877 (HGNC:27706): (long intergenic non-protein coding RNA 877)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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
LINC00877	ENST00000626474.3	n.456-27364A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48309 AN: 151900 Hom.: 7824 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.318 AC: 48348 AN: 152018 Hom.: 7832 Cov.: 32 AF XY: 0.316 AC XY: 23453 AN XY: 74306

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.319

Alfa AF: 0.317 Hom.: 922

Bravo AF: 0.312

Asia WGS AF: 0.237 AC: 825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	17
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1316386; hg19: chr3-72176525;