rs2135319

Positions:

• chr3-71974549-G-A

Variant summary

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

The ENST00000666244.1(LINC00877):​n.1223-575C>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 0.0911 in 152,076 control chromosomes in the GnomAD database, including 650 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 0.091 (650 hom., cov: 32)
• Consequence: LINC00877 ENST00000666244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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 (EAS) allele frequency at 95% confidence interval = 0.181 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	ENST00000666244.1	n.1223-575C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13845 AN: 151958 Hom.: 649 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0911 AC: 13849 AN: 152076 Hom.: 650 Cov.: 32 AF XY: 0.0898 AC XY: 6677 AN XY: 74352

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0860 Hom.: 114

Bravo AF: 0.0937

Asia WGS AF: 0.132 AC: 458 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	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2135319; hg19: chr3-72023700;