17-27754938-A-G

Position:

• chr17-27754938-A-G

Variant summary

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

The ENST00000580112.1(LGALS9DP):​n.748A>G 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 0.629 in 745,190 control chromosomes in the GnomAD database, including 150,774 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 0.66 (33736 hom., cov: 31)
  • Exomes 𝑓: 0.62 (117038 hom.)
• Consequence: LGALS9DP ENST00000580112.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS9DP	ENST00000580112.1	n.748A>G		non_coding_transcript_exon_variant	8/8

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99941 AN: 151862 Hom.: 33684 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.670

GnomAD4 exome AF: 0.622 AC: 368827 AN: 593212 Hom.: 117038 Cov.: 7 AF XY: 0.632 AC XY: 200856 AN XY: 317924

Gnomad4 AFR exome AF: 0.815

Gnomad4 AMR exome AF: 0.601

Gnomad4 ASJ exome AF: 0.647

Gnomad4 EAS exome AF: 0.718

Gnomad4 SAS exome AF: 0.799

Gnomad4 FIN exome AF: 0.564

Gnomad4 NFE exome AF: 0.582

Gnomad4 OTH exome AF: 0.629

GnomAD4 genome AF: 0.658 AC: 100052 AN: 151978 Hom.: 33736 Cov.: 31 AF XY: 0.662 AC XY: 49139 AN XY: 74268

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.673

Alfa AF: 0.610 Hom.: 4316

Bravo AF: 0.663

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
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: rs8081248; hg19: chr17-26081964;