3-157121142-G-C

Position:

• chr3-157121142-G-C

Variant summary

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

The NR_034007.1(LINC00880):​n.127+1734C>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 0.0499 in 152,128 control chromosomes in the GnomAD database, including 468 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 0.050 (468 hom., cov: 33)
• Consequence: LINC00880 NR_034007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

LINC00880 (HGNC:27948): (long intergenic non-protein coding RNA 880)

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00880	NR_034007.1	n.127+1734C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00880	ENST00000471357.1	n.129+1734C>G		intron_variant, non_coding_transcript_variant		1
LINC00880	ENST00000659739.1	n.290+1734C>G		intron_variant, non_coding_transcript_variant
LINC00881	ENST00000665438.1	n.305-12900G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7588 AN: 152010 Hom.: 467 Cov.: 33

Gnomad AFR AF: 0.00944

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0499 AC: 7591 AN: 152128 Hom.: 468 Cov.: 33 AF XY: 0.0548 AC XY: 4072 AN XY: 74364

Gnomad4 AFR AF: 0.00937

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0204 Hom.: 8

Bravo AF: 0.0500

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12490016; hg19: chr3-156838931;