rs2030665

chr2-129256416-T-Achr2-129256416-T-C

Variant summary

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

The NR_122041.1(LINC01854):n.286-6342A>T 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 0.0184 in 152,272 control chromosomes in the GnomAD database, including 171 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 0.018 (171 hom., cov: 32)
• Consequence: LINC01854 NR_122041.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01854	NR_122041.1	n.286-6342A>T		intron_variant, non_coding_transcript_variant
LINC01854	NR_122040.1	n.286-6342A>T		intron_variant, non_coding_transcript_variant
LINC01854	NR_122042.1	n.286-6342A>T		intron_variant, non_coding_transcript_variant
LOC105373612	XR_007087234.1	n.276+9897T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01854	ENST00000375987.3	n.243-6342A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2790 AN: 152152 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.00444

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00188

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0184 AC: 2804 AN: 152272 Hom.: 171 Cov.: 32 AF XY: 0.0210 AC XY: 1564 AN XY: 74434

Gnomad4 AFR AF: 0.00457

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0700

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00187

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.00107 Hom.: 1

Bravo AF: 0.0243

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.8
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030665; hg19: chr2-130013989;