2-129242309-C-T

Variant names:

• chr2-129242309-C-T
• rs1251175
• ENST00000375987.3:n.2077G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LINC01854 (HGNC:52670): (long intergenic non-protein coding RNA 1854)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375987.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01854	NR_122040.1		n.2120G>A		non_coding_transcript_exon	Exon 5 of 5
	LINC01854	NR_122041.1		n.2032G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01854	NR_122042.1		n.2043G>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01854	ENST00000375987.3	TSL:2	n.2077G>A		non_coding_transcript_exon	Exon 5 of 5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.951 AC: 135 AN: 142

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.852 AC: 35372 AN: 41524

American (AMR) AF: 0.977 AC: 14950 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3288 AN: 3470

East Asian (EAS) AF: 0.966 AC: 5000 AN: 5176

South Asian (SAS) AF: 0.857 AC: 4129 AN: 4816

European-Finnish (FIN) AF: 0.938 AC: 9943 AN: 10602

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66330 AN: 68044

Other (OTH) AF: 0.947 AC: 2001 AN: 2112

Alfa AF: 0.956 Hom.: 30507

Bravo AF: 0.936

Asia WGS AF: 0.908 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1251175; hg19: chr2-129999882;