chr10-78385678-C-T

Variant names:

• chr10-78385678-C-T
• rs719871
• ENST00000421324.4:n.51-143073C>T

Variant summary

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

The ENST00000421324.4(LINC00856):​n.51-143073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,172 control chromosomes in the GnomAD database, including 867 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 0.11 (867 hom., cov: 32)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 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.51-143073C>T		intron_variant	Intron 1 of 2	1
LINC00856	ENST00000624665.3	n.331+136608C>T		intron_variant	Intron 1 of 3	2
LINC00856	ENST00000634389.1	n.408-10733C>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16075 AN: 152054 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.106 AC: 16098 AN: 152172 Hom.: 867 Cov.: 32 AF XY: 0.108 AC XY: 7998 AN XY: 74374

African (AFR) AF: 0.112 AC: 4668 AN: 41522

American (AMR) AF: 0.133 AC: 2030 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5164

South Asian (SAS) AF: 0.108 AC: 518 AN: 4814

European-Finnish (FIN) AF: 0.0942 AC: 997 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6806 AN: 68008

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.106 Hom.: 464

Bravo AF: 0.106

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.57
PhyloP100		-2.0

Splicing

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

Publications

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Other links and lift over

dbSNP: rs719871; hg19: chr10-80145435;