17-27748474-T-C

Variant summary

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

The ENST00000580112.1(LGALS9DP):n.317+146T>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 0.509 in 472,502 control chromosomes in the GnomAD database, including 63,544 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 0.56 (24777 hom., cov: 32)
  • Exomes 𝑓: 0.49 (38767 hom.)
• Consequence: LGALS9DP ENST00000580112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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.317+146T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84402 AN: 151916 Hom.: 24752 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.558

GnomAD4 exome AF: 0.487 AC: 156180 AN: 320468 Hom.: 38767 AF XY: 0.489 AC XY: 88625 AN XY: 181076

Gnomad4 AFR exome AF: 0.753

Gnomad4 AMR exome AF: 0.537

Gnomad4 ASJ exome AF: 0.482

Gnomad4 EAS exome AF: 0.504

Gnomad4 SAS exome AF: 0.529

Gnomad4 FIN exome AF: 0.453

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.492

GnomAD4 genome AF: 0.556 AC: 84468 AN: 152034 Hom.: 24777 Cov.: 32 AF XY: 0.555 AC XY: 41257 AN XY: 74288

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.551

Alfa AF: 0.506 Hom.: 2544

Bravo AF: 0.572

Asia WGS AF: 0.488 AC: 1700 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	1.6
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7215373; hg19: chr17-26075500;