chr10-78488998-T-C

Variant names:

• chr10-78488998-T-C
• rs1369752
• ENST00000421324.4:n.51-39753T>C

Variant summary

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

The ENST00000421324.4(LINC00856):​n.51-39753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,126 control chromosomes in the GnomAD database, including 9,155 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 0.31 (9155 hom., cov: 33)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421324.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00856	ENST00000421324.4	TSL:1	n.51-39753T>C		intron	N/A
	LINC00856	ENST00000510550.2	TSL:4	n.157-36332T>C		intron	N/A
	LINC00856	ENST00000624665.3	TSL:2	n.332-36332T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47736 AN: 152006 Hom.: 9117 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47823 AN: 152126 Hom.: 9155 Cov.: 33 AF XY: 0.314 AC XY: 23355 AN XY: 74362

African (AFR) AF: 0.541 AC: 22429 AN: 41482

American (AMR) AF: 0.297 AC: 4544 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5170

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10576

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13617 AN: 67998

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.241 Hom.: 21602

Bravo AF: 0.327

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1369752; hg19: chr10-80248755;