17-27754003-C-G

Position:

• chr17-27754003-C-G

Variant summary

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

The ENST00000580112.1(LGALS9DP):​n.516-83C>G 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 0.25 in 1,482,516 control chromosomes in the GnomAD database, including 47,530 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 0.24 (4471 hom., cov: 32)
  • Exomes 𝑓: 0.25 (43059 hom.)
• Consequence: LGALS9DP ENST00000580112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

LGALS9DP (HGNC:49896): (galectin 9D, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS9DP	ENST00000580112.1	n.516-83C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36471 AN: 152022 Hom.: 4472 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.251 AC: 334252 AN: 1330378 Hom.: 43059 AF XY: 0.254 AC XY: 169863 AN XY: 668298

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.327

Gnomad4 ASJ exome AF: 0.263

Gnomad4 EAS exome AF: 0.291

Gnomad4 SAS exome AF: 0.342

Gnomad4 FIN exome AF: 0.209

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.240 AC: 36493 AN: 152138 Hom.: 4471 Cov.: 32 AF XY: 0.240 AC XY: 17832 AN XY: 74394

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.264

Alfa AF: 0.123 Hom.: 190

Bravo AF: 0.244

Asia WGS AF: 0.278 AC: 966 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9901734; hg19: chr17-26081029; COSMIC: COSV58224149;