ENST00000455711.1:n.176-1201A>G

Variant names:

• chr20-63047655-A-G
• rs11698703
• ENST00000455711.1:n.176-1201A>G

Variant summary

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

The ENST00000455711.1(LINC01056):​n.176-1201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 152,248 control chromosomes in the GnomAD database, including 651 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 0.079 (651 hom., cov: 32)
• Consequence: LINC01056 ENST00000455711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 4 publications found

Genes affected

LINC01056 (HGNC:49050): (long intergenic non-protein coding RNA 1056)

LINC01749 (HGNC:52537): (long intergenic non-protein coding RNA 1749)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01056	NR_033369.1	n.176-1201A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01056	ENST00000455711.1	n.176-1201A>G		intron_variant	Intron 1 of 5	1
LINC01749	ENST00000606208.5	n.92-35627A>G		intron_variant	Intron 1 of 1	1
LINC01749	ENST00000607802.1	n.92-32337A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 12026 AN: 152130 Hom.: 651 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0790 AC: 12023 AN: 152248 Hom.: 651 Cov.: 32 AF XY: 0.0775 AC XY: 5769 AN XY: 74438

African (AFR) AF: 0.0226 AC: 938 AN: 41558

American (AMR) AF: 0.0695 AC: 1062 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1190 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8227 AN: 68006

Other (OTH) AF: 0.0802 AC: 169 AN: 2108

Alfa AF: 0.0911 Hom.: 580

Bravo AF: 0.0715

Asia WGS AF: 0.0140 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11698703; hg19: chr20-61679007;