3-72112082-T-A

Position:

• chr3-72112082-T-A

Variant summary

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

The ENST00000626474.3(LINC00877):​n.456-12072A>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 0.545 in 152,128 control chromosomes in the GnomAD database, including 23,518 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 0.54 (23518 hom., cov: 33)
• Consequence: LINC00877 ENST00000626474.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00877	ENST00000626474.3	n.456-12072A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82775 AN: 152010 Hom.: 23479 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.545 AC: 82865 AN: 152128 Hom.: 23518 Cov.: 33 AF XY: 0.545 AC XY: 40522 AN XY: 74388

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.559

Alfa AF: 0.503 Hom.: 2409

Bravo AF: 0.553

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6549438; hg19: chr3-72161233;