ENST00000469218.6:n.149-38108A>G

Variant names:

• chr3-72138118-T-C
• rs6802792
• ENST00000469218.6:n.149-38108A>G

Variant summary

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

The ENST00000469218.6(LINC00877):​n.149-38108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,170 control chromosomes in the GnomAD database, including 4,467 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 0.14 (4467 hom., cov: 32)
• Consequence: LINC00877 ENST00000469218.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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
LINC00877	ENST00000469218.6	n.149-38108A>G		intron_variant	Intron 2 of 8	5
LINC00877	ENST00000481148.5	n.132-38108A>G		intron_variant	Intron 1 of 2	4
LINC00877	ENST00000626474.3	n.456-38108A>G		intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21627 AN: 152052 Hom.: 4438 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.143 AC: 21725 AN: 152170 Hom.: 4467 Cov.: 32 AF XY: 0.141 AC XY: 10513 AN XY: 74406

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.0610

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.00323

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0332 Hom.: 763

Bravo AF: 0.162

Asia WGS AF: 0.100 AC: 348 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	1.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6802792; hg19: chr3-72187269;