chr3-182032653-G-A

Variant names:

• chr3-182032653-G-A
• rs10513785
• ENST00000654747.1:n.889-2708G>A

Variant summary

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

The ENST00000654747.1(LINC01206):​n.889-2708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,086 control chromosomes in the GnomAD database, including 3,442 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 (3442 hom., cov: 32)
• Consequence: LINC01206 ENST00000654747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 0 publications found

Genes affected

LINC01206 (HGNC:49637): (long intergenic non-protein coding RNA 1206)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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
LINC01206	ENST00000654747.1	n.889-2708G>A		intron_variant	Intron 5 of 5
LINC01206	ENST00000666871.1	n.1534-2708G>A		intron_variant	Intron 9 of 9
LINC01206	ENST00000716321.1	n.1253-19129G>A		intron_variant	Intron 7 of 8
LINC01206	ENST00000764327.1	n.695-2708G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17561 AN: 151968 Hom.: 3420 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00149

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.116 AC: 17639 AN: 152086 Hom.: 3442 Cov.: 32 AF XY: 0.112 AC XY: 8346 AN XY: 74366

African (AFR) AF: 0.405 AC: 16791 AN: 41446

American (AMR) AF: 0.0369 AC: 563 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00149 AC: 101 AN: 67982

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0674 Hom.: 231

Bravo AF: 0.130

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10513785; hg19: chr3-181750441;