rs10740479

Variant names:

• chr10-78462711-G-A
• rs10740479
• ENST00000421324.4:n.51-66040G>A

Variant summary

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

The ENST00000421324.4(LINC00856):​n.51-66040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,092 control chromosomes in the GnomAD database, including 1,310 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 0.12 (1310 hom., cov: 32)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 4 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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.51-66040G>A		intron_variant	Intron 1 of 2	1
LINC00856	ENST00000510550.2	n.156+56012G>A		intron_variant	Intron 1 of 3	4
LINC00856	ENST00000624665.3	n.332-62619G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18424 AN: 151974 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.121 AC: 18437 AN: 152092 Hom.: 1310 Cov.: 32 AF XY: 0.122 AC XY: 9104 AN XY: 74356

African (AFR) AF: 0.0469 AC: 1948 AN: 41500

American (AMR) AF: 0.185 AC: 2823 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1080 AN: 5150

South Asian (SAS) AF: 0.113 AC: 547 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1426 AN: 10570

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9768 AN: 67990

Other (OTH) AF: 0.122 AC: 257 AN: 2106

Alfa AF: 0.121 Hom.: 854

Bravo AF: 0.120

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.8
DANN	Benign	0.95
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs10740479; hg19: chr10-80222468;