3-72138118-T-C

Position:

• chr3-72138118-T-C

Variant summary

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

The ENST00000626474.3(LINC00877):​n.456-38108A>G 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 0.143 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 ENST00000626474.3 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00877	ENST00000626474.3	n.456-38108A>G		intron_variant, non_coding_transcript_variant		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;