rs12359728

Variant names:

• chr10-108296563-A-G
• rs12359728
• ENST00000809134.1:n.231-98715T>C

Variant summary

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

The ENST00000809134.1(LINC01435):​n.231-98715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,614 control chromosomes in the GnomAD database, including 265 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 0.037 (265 hom., cov: 32)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: LINC01435 ENST00000809134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• Publications: 0 publications found

Genes affected

LINC01435 (HGNC:50753): (long intergenic non-protein coding RNA 1435)

PTGES3P5 (HGNC:43826): (prostaglandin E synthase 3 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 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
LINC01435	ENST00000809134.1	n.231-98715T>C		intron_variant	Intron 2 of 3
PTGES3P5	ENST00000455109.2	n.*31A>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5639 AN: 152130 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.00763

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.00678

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0446

GnomAD4 exome AF: 0.0109 AC: 4 AN: 366 Hom.: 0 Cov.: 0 AF XY: 0.0169 AC XY: 3 AN XY: 178

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00824 AC: 3 AN: 364

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0371 AC: 5656 AN: 152248 Hom.: 265 Cov.: 32 AF XY: 0.0395 AC XY: 2937 AN XY: 74440

African (AFR) AF: 0.00760 AC: 316 AN: 41564

American (AMR) AF: 0.0910 AC: 1390 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3470

East Asian (EAS) AF: 0.171 AC: 882 AN: 5168

South Asian (SAS) AF: 0.124 AC: 600 AN: 4826

European-Finnish (FIN) AF: 0.00678 AC: 72 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2199 AN: 68014

Other (OTH) AF: 0.0441 AC: 93 AN: 2108

Alfa AF: 0.0310 Hom.: 18

Bravo AF: 0.0425

Asia WGS AF: 0.137 AC: 473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.70
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs12359728; hg19: chr10-110056321;