rs1524187

chr2-129262910-A-G

Variant summary

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

The NR_122041.1(LINC01854):n.285+10697T>C 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 0.0197 in 152,300 control chromosomes in the GnomAD database, including 172 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 0.020 (172 hom., cov: 32)
• Consequence: LINC01854 NR_122041.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

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

LOC105373612 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01854	NR_122041.1	n.285+10697T>C		intron_variant, non_coding_transcript_variant
LINC01854	NR_122040.1	n.285+10697T>C		intron_variant, non_coding_transcript_variant
LINC01854	NR_122042.1	n.285+10697T>C		intron_variant, non_coding_transcript_variant
LOC105373612	XR_007087234.1	n.276+16391A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01854	ENST00000375987.3	n.242+10697T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2989 AN: 152180 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.00861

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00198

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0197 AC: 3007 AN: 152300 Hom.: 172 Cov.: 32 AF XY: 0.0223 AC XY: 1664 AN XY: 74460

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00197

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.00894 Hom.: 118

Bravo AF: 0.0259

Asia WGS AF: 0.124 AC: 433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.51
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524187; hg19: chr2-130020483;