2-129242309-C-T

Position:

• chr2-129242309-C-T

Variant summary

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

The ENST00000375987.3(LINC01854):​n.2077G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 152,398 control chromosomes in the GnomAD database, including 66,714 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 0.93 (66650 hom., cov: 32)
  • Exomes 𝑓: 0.95 (64 hom.)
• Consequence: LINC01854 ENST00000375987.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

LINC01854 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01854	NR_122040.1	n.2120G>A		non_coding_transcript_exon_variant	5/5
LINC01854	NR_122041.1	n.2032G>A		non_coding_transcript_exon_variant	4/4
LINC01854	NR_122042.1	n.2043G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01854	ENST00000375987.3	n.2077G>A		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142085 AN: 152138 Hom.: 66606 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.949

GnomAD4 exome AF: 0.951 AC: 135 AN: 142 Hom.: 64 Cov.: 0 AF XY: 0.939 AC XY: 77 AN XY: 82

Gnomad4 FIN exome AF: 0.951

GnomAD4 genome AF: 0.934 AC: 142184 AN: 152256 Hom.: 66650 Cov.: 32 AF XY: 0.932 AC XY: 69358 AN XY: 74434

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.947

Alfa AF: 0.956 Hom.: 26603

Bravo AF: 0.936

Asia WGS AF: 0.908 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1251175; hg19: chr2-129999882;