chr10-78521979-G-A

Variant names:

• chr10-78521979-G-A
• rs2019080
• ENST00000421324.4:n.51-6772G>A

Variant summary

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

The ENST00000421324.4(LINC00856):​n.51-6772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,910 control chromosomes in the GnomAD database, including 19,206 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 0.49 (19206 hom., cov: 32)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 3 publications found

Genes affected

LINC00856 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 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
LINC00856	ENST00000421324.4	n.51-6772G>A		intron_variant	Intron 1 of 2	1
LINC00856	ENST00000510550.2	n.157-3351G>A		intron_variant	Intron 1 of 3	4
LINC00856	ENST00000624665.3	n.332-3351G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74984 AN: 151792 Hom.: 19200 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.494 AC: 75012 AN: 151910 Hom.: 19206 Cov.: 32 AF XY: 0.488 AC XY: 36217 AN XY: 74236

African (AFR) AF: 0.459 AC: 19022 AN: 41410

American (AMR) AF: 0.483 AC: 7371 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.0381 AC: 197 AN: 5164

South Asian (SAS) AF: 0.369 AC: 1770 AN: 4798

European-Finnish (FIN) AF: 0.560 AC: 5902 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37522 AN: 67946

Other (OTH) AF: 0.479 AC: 1010 AN: 2108

Alfa AF: 0.505 Hom.: 3305

Bravo AF: 0.487

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2019080; hg19: chr10-80281736;