chr10-78586629-T-G

Variant names:

• chr10-78586629-T-G
• rs844429
• ENST00000421324.4:n.114+57815T>G

Variant summary

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

The ENST00000421324.4(LINC00856):​n.114+57815T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,128 control chromosomes in the GnomAD database, including 7,077 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 0.23 (7077 hom., cov: 32)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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.114+57815T>G		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35177 AN: 152006 Hom.: 7046 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.232 AC: 35266 AN: 152128 Hom.: 7077 Cov.: 32 AF XY: 0.226 AC XY: 16843 AN XY: 74368

African (AFR) AF: 0.546 AC: 22637 AN: 41448

American (AMR) AF: 0.197 AC: 3005 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.179 AC: 927 AN: 5176

South Asian (SAS) AF: 0.190 AC: 915 AN: 4828

European-Finnish (FIN) AF: 0.0389 AC: 413 AN: 10610

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6368 AN: 68000

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.172 Hom.: 545

Bravo AF: 0.255

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.42
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs844429; hg19: chr10-80346386;