3-95121599-C-T

Position:

• chr3-95121599-C-T

Variant summary

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

The ENST00000665896.1(LINC00879):​n.485-16587C>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 0.168 in 152,150 control chromosomes in the GnomAD database, including 2,485 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 0.17 (2485 hom., cov: 32)
• Consequence: LINC00879 ENST00000665896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

Genes affected

LINC00879 (HGNC:48566): (long intergenic non-protein coding RNA 879)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 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
LINC00879	ENST00000665896.1	n.485-16587C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25570 AN: 152032 Hom.: 2477 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.168 AC: 25591 AN: 152150 Hom.: 2485 Cov.: 32 AF XY: 0.173 AC XY: 12830 AN XY: 74374

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.168

Alfa AF: 0.143 Hom.: 1605

Bravo AF: 0.162

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3849439; hg19: chr3-94840443;