ENST00000375987.3:n.242+10763G>C

Variant names:

• chr2-129262844-C-G
• rs1524186
• ENST00000375987.3:n.242+10763G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375987.3(LINC01854):​n.242+10763G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,116 control chromosomes in the GnomAD database, including 272 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 0.035 (272 hom., cov: 32)
• Consequence: LINC01854 ENST00000375987.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 publications found

Genes affected

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

LOC105373612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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.285+10763G>C		intron	N/A
	LINC01854	NR_122041.1		n.285+10763G>C		intron	N/A
	LINC01854	NR_122042.1		n.285+10763G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01854	ENST00000375987.3	TSL:2	n.242+10763G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5377 AN: 151996 Hom.: 271 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00216

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0355 AC: 5396 AN: 152116 Hom.: 272 Cov.: 32 AF XY: 0.0382 AC XY: 2839 AN XY: 74372

African (AFR) AF: 0.0633 AC: 2625 AN: 41492

American (AMR) AF: 0.0750 AC: 1145 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3470

East Asian (EAS) AF: 0.191 AC: 986 AN: 5162

South Asian (SAS) AF: 0.0703 AC: 338 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00215 AC: 146 AN: 68000

Other (OTH) AF: 0.0365 AC: 77 AN: 2112

Alfa AF: 0.00355 Hom.: 2

Bravo AF: 0.0440

Asia WGS AF: 0.127 AC: 440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.36
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1524186; hg19: chr2-130020417;