ENST00000838855.1:n.99-18206G>A

Variant names:

• chr12-9228263-G-A
• rs10771431
• ENST00000838855.1:n.99-18206G>A

Variant summary

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

The ENST00000838855.1(LINC00987):​n.99-18206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,034 control chromosomes in the GnomAD database, including 13,410 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 0.42 (13410 hom., cov: 33)
• Consequence: LINC00987 ENST00000838855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 16 publications found

Genes affected

LINC00987 (HGNC:48911): (long intergenic non-protein coding RNA 987)

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 = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00987	ENST00000838855.1	n.99-18206G>A		intron_variant	Intron 1 of 5
LINC00987	ENST00000838856.1	n.144-18206G>A		intron_variant	Intron 1 of 3
LINC00987	ENST00000838857.1	n.143-18206G>A		intron_variant	Intron 2 of 4
LINC00987	ENST00000838858.1	n.143-12022G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63247 AN: 151916 Hom.: 13410 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.416 AC: 63263 AN: 152034 Hom.: 13410 Cov.: 33 AF XY: 0.414 AC XY: 30754 AN XY: 74304

African (AFR) AF: 0.366 AC: 15183 AN: 41452

American (AMR) AF: 0.383 AC: 5843 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3531 AN: 5178

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4822

European-Finnish (FIN) AF: 0.368 AC: 3886 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29989 AN: 67974

Other (OTH) AF: 0.438 AC: 925 AN: 2114

Alfa AF: 0.437 Hom.: 39249

Bravo AF: 0.419

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10771431; hg19: chr12-9380859;