rs10507272

Variant names:

• chr12-116685571-G-A
• rs10507272
• ENST00000546835.2:n.762-12284G>A

Variant summary

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

The ENST00000546835.2(LINC03088):​n.762-12284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,068 control chromosomes in the GnomAD database, including 21,579 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 0.50 (21579 hom., cov: 32)
• Consequence: LINC03088 ENST00000546835.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 3 publications found

Genes affected

LINC03088 (HGNC:56710): (long intergenic non-protein coding RNA 3088)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03088	XR_007063473.1	n.704-12284G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03088	ENST00000546835.2	n.762-12284G>A		intron_variant	Intron 1 of 1	3
LINC03088	ENST00000730135.1	n.704-17222G>A		intron_variant	Intron 1 of 1
LINC03088	ENST00000730136.1	n.762-7549G>A		intron_variant	Intron 1 of 1
LINC03088	ENST00000730137.1	n.183-7549G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76590 AN: 151952 Hom.: 21563 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.504 AC: 76617 AN: 152068 Hom.: 21579 Cov.: 32 AF XY: 0.513 AC XY: 38123 AN XY: 74314

African (AFR) AF: 0.263 AC: 10928 AN: 41484

American (AMR) AF: 0.511 AC: 7800 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4943 AN: 5178

South Asian (SAS) AF: 0.754 AC: 3639 AN: 4828

European-Finnish (FIN) AF: 0.649 AC: 6852 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38933 AN: 67972

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.547 Hom.: 62358

Bravo AF: 0.483

Asia WGS AF: 0.772 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.48
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10507272; hg19: chr12-117123376;