rs2699066

Positions:

• chr12-127912871-A-G

Variant summary

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

The NR_126452.2(LINC00508):​n.311+27703T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,154 control chromosomes in the GnomAD database, including 3,376 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 0.16 (3376 hom., cov: 33)
• Consequence: LINC00508 NR_126452.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

LINC00508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00508	NR_126452.2	n.311+27703T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24105 AN: 152036 Hom.: 3371 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.159 AC: 24137 AN: 152154 Hom.: 3376 Cov.: 33 AF XY: 0.156 AC XY: 11617 AN XY: 74412

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.0753

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.128

Alfa AF: 0.115 Hom.: 317

Bravo AF: 0.173

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2699066; hg19: chr12-128397416;