rs6487679

Variant names:

• chr12-9218736-C-T
• rs6487679
• ENST00000838855.1:n.99-27733C>T

Variant summary

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

The ENST00000838855.1(LINC00987):​n.99-27733C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,150 control chromosomes in the GnomAD database, including 49,341 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 0.80 (49341 hom., cov: 33)
• Consequence: LINC00987 ENST00000838855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 20 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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.99-27733C>T		intron_variant	Intron 1 of 5
LINC00987	ENST00000838856.1	n.144-27733C>T		intron_variant	Intron 1 of 3
LINC00987	ENST00000838857.1	n.143-27733C>T		intron_variant	Intron 2 of 4
LINC00987	ENST00000838858.1	n.143-21549C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122273 AN: 152032 Hom.: 49287 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.804 AC: 122382 AN: 152150 Hom.: 49341 Cov.: 33 AF XY: 0.804 AC XY: 59836 AN XY: 74390

African (AFR) AF: 0.755 AC: 31306 AN: 41486

American (AMR) AF: 0.862 AC: 13172 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2825 AN: 3468

East Asian (EAS) AF: 0.883 AC: 4578 AN: 5186

South Asian (SAS) AF: 0.741 AC: 3570 AN: 4820

European-Finnish (FIN) AF: 0.812 AC: 8610 AN: 10600

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55565 AN: 67984

Other (OTH) AF: 0.823 AC: 1742 AN: 2116

Alfa AF: 0.816 Hom.: 180823

Bravo AF: 0.811

Asia WGS AF: 0.830 AC: 2887 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.25
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs6487679; hg19: chr12-9371332;