chr2-19878380-A-G

Variant names:

• chr2-19878380-A-G
• rs13028359
• ENST00000449086.5:n.921-856A>G

Variant summary

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

The ENST00000449086.5(LINC00954):​n.921-856A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,182 control chromosomes in the GnomAD database, including 7,379 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 0.29 (7379 hom., cov: 33)
• Consequence: LINC00954 ENST00000449086.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 6 publications found

Genes affected

LINC00954 (HGNC:48668): (long intergenic non-protein coding RNA 954)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00954	NR_033875.1	n.941-856A>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00954	ENST00000449086.5	n.921-856A>G		intron_variant	Intron 6 of 9	1
LINC00954	ENST00000649549.1	n.579-731A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44325 AN: 152064 Hom.: 7381 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.291 AC: 44319 AN: 152182 Hom.: 7379 Cov.: 33 AF XY: 0.286 AC XY: 21260 AN XY: 74412

African (AFR) AF: 0.144 AC: 5973 AN: 41526

American (AMR) AF: 0.323 AC: 4944 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3468

East Asian (EAS) AF: 0.0897 AC: 464 AN: 5172

South Asian (SAS) AF: 0.188 AC: 907 AN: 4834

European-Finnish (FIN) AF: 0.370 AC: 3923 AN: 10590

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25667 AN: 67976

Other (OTH) AF: 0.298 AC: 629 AN: 2112

Alfa AF: 0.349 Hom.: 8795

Bravo AF: 0.285

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.70
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs13028359; hg19: chr2-20078141;