rs886599

Variant names:

• chr14-70707727-C-T
• rs886599
• ENST00000799794.1:n.201G>A

Variant summary

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

The ENST00000799794.1(ENSG00000304105):​n.201G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,080 control chromosomes in the GnomAD database, including 5,046 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 0.25 (5046 hom., cov: 32)
• Consequence: ENSG00000304105 ENST00000799794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 7 publications found

Genes affected

ENSG00000304105 (HGNC:):

LINC01269 (HGNC:50325): (long intergenic non-protein coding RNA 1269)

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 (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01269	NR_125769.1	n.458+3940C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304105	ENST00000799794.1	n.201G>A		non_coding_transcript_exon_variant	Exon 2 of 3
LINC01269	ENST00000553682.2	n.634+3940C>T		intron_variant	Intron 3 of 3	4
LINC01269	ENST00000702053.2	n.303-4283C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38663 AN: 151962 Hom.: 5041 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.254 AC: 38696 AN: 152080 Hom.: 5046 Cov.: 32 AF XY: 0.260 AC XY: 19330 AN XY: 74342

African (AFR) AF: 0.262 AC: 10882 AN: 41474

American (AMR) AF: 0.260 AC: 3970 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.148 AC: 766 AN: 5168

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4820

European-Finnish (FIN) AF: 0.393 AC: 4149 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16544 AN: 67970

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.244 Hom.: 8320

Bravo AF: 0.244

Asia WGS AF: 0.221 AC: 772 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	0.18
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs886599; hg19: chr14-71174444;