20-11872507-A-G

Variant names:

• chr20-11872507-A-G
• rs803880
• ENST00000427835.3:n.186-314T>C

Variant summary

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

The ENST00000427835.3(LINC00687):​n.186-314T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,004 control chromosomes in the GnomAD database, including 13,335 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 (13335 hom., cov: 32)
• Consequence: LINC00687 ENST00000427835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 1 publications found

Genes affected

LINC00687 (HGNC:16194): (long intergenic non-protein coding RNA 687)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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
LINC00687	ENST00000427835.3	n.186-314T>C		intron_variant	Intron 2 of 5	3
LINC00687	ENST00000656506.1	n.119-1780T>C		intron_variant	Intron 1 of 2
LINC00687	ENST00000666572.1	n.177-314T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63375 AN: 151886 Hom.: 13325 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.417 AC: 63409 AN: 152004 Hom.: 13335 Cov.: 32 AF XY: 0.414 AC XY: 30746 AN XY: 74284

African (AFR) AF: 0.463 AC: 19201 AN: 41454

American (AMR) AF: 0.376 AC: 5740 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1377 AN: 5160

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4810

European-Finnish (FIN) AF: 0.427 AC: 4501 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27751 AN: 67964

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.393 Hom.: 5938

Bravo AF: 0.412

Asia WGS AF: 0.337 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.56
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs803880; hg19: chr20-11853155;