chr2-129256416-T-A

Variant names:

• chr2-129256416-T-A
• rs2030665
• ENST00000375987.3:n.243-6342A>T

Variant summary

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

The ENST00000375987.3(LINC01854):​n.243-6342A>T variant causes a intron 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 ENST00000375987.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 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.286-6342A>T		intron	N/A
	LINC01854	NR_122041.1		n.286-6342A>T		intron	N/A
	LINC01854	NR_122042.1		n.286-6342A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01854	ENST00000375987.3	TSL:2	n.243-6342A>T		intron	N/A

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

African (AFR) AF: 0.00457 AC: 190 AN: 41570

American (AMR) AF: 0.0692 AC: 1058 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.193 AC: 997 AN: 5172

South Asian (SAS) AF: 0.0700 AC: 337 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00187 AC: 127 AN: 68018

Other (OTH) AF: 0.0218 AC: 46 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2030665; hg19: chr2-130013989;