rs8081248

Variant names:

• chr17-27754938-A-G
• rs8081248
• ENST00000580112.1:n.748A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-27754938-A-G
• chr17-27754938-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LGALS9DP		n.27754938A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS9DP	ENST00000580112.1	n.748A>G		non_coding_transcript_exon_variant	Exon 8 of 8	6

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

African (AFR) AF: 0.815 AC: 12573 AN: 15424

American (AMR) AF: 0.601 AC: 21764 AN: 36196

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 8828 AN: 13638

East Asian (EAS) AF: 0.718 AC: 12091 AN: 16832

South Asian (SAS) AF: 0.799 AC: 55957 AN: 70066

European-Finnish (FIN) AF: 0.564 AC: 18473 AN: 32726

Middle Eastern (MID) AF: 0.751 AC: 1430 AN: 1904

European-Non Finnish (NFE) AF: 0.582 AC: 222166 AN: 381710

Other (OTH) AF: 0.629 AC: 15545 AN: 24716

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

African (AFR) AF: 0.798 AC: 33109 AN: 41470

American (AMR) AF: 0.648 AC: 9902 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3562 AN: 5154

South Asian (SAS) AF: 0.803 AC: 3852 AN: 4798

European-Finnish (FIN) AF: 0.576 AC: 6082 AN: 10550

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39035 AN: 67944

Other (OTH) AF: 0.673 AC: 1417 AN: 2106

Alfa AF: 0.631 Hom.: 5668

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs8081248; hg19: chr17-26081964;