rs2699089

Variant names:

• chr12-127919658-T-C
• rs2699089
• ENST00000542089.2:n.383+3976T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000542089.2(LINC00507):​n.383+3976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,530 control chromosomes in the GnomAD database, including 1,925 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 0.13 (1925 hom., cov: 32)
• Consequence: LINC00507 ENST00000542089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

Genes affected

LINC00507 (HGNC:43558): (long intergenic non-protein coding RNA 507)

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00507	NR_046392.1	n.273+3976T>C		intron_variant	Intron 1 of 4
LINC00508	NR_126452.2	n.311+20916A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00507	ENST00000542089.2	n.383+3976T>C		intron_variant	Intron 1 of 3	1
LINC00507	ENST00000540882.6	n.251+3976T>C		intron_variant	Intron 1 of 4	5
LINC00507	ENST00000544645.6	n.276+3976T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20039 AN: 151412 Hom.: 1916 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0232

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00711

Gnomad SAS AF: 0.0407

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.132 AC: 20069 AN: 151530 Hom.: 1925 Cov.: 32 AF XY: 0.129 AC XY: 9584 AN XY: 74086

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00713

Gnomad4 SAS AF: 0.0410

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0915 Hom.: 1041

Bravo AF: 0.138

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2699089; hg19: chr12-128404203;