Variant rs8103033 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_034156.1(LGALS17A):n.40G>A 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 0.295 in 170,306 control chromosomes in the GnomAD database, including 8,429 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 0.29 ( 7290 hom., cov: 32)

Exomes 𝑓: 0.35 ( 1139 hom. )

Consequence

LGALS17A
NR_034156.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170

Variant links:

Genes affected

LGALS17A (HGNC:):

LGALS17A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS17A	NR_034156.1 linkuse as main transcript	n.40G>A		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS17A	ENST00000412609.5 linkuse as main transcript	n.40G>A		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43802

AN:

151984

Hom.:

7278

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.317

GnomAD4 exome

AF:

0.351

AC:

6384

AN:

18204

Hom.:

1139

Cov.:

AF XY:

0.350

AC XY:

3052

AN XY:

8716

show subpopulations

Gnomad4 AFR exome

AF:

0.200

Gnomad4 AMR exome

AF:

0.667

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.335

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.288

AC:

43830

AN:

152102

Hom.:

7290

Cov.:

AF XY:

0.289

AC XY:

21508

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.303

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.324

Hom.:

12192

Bravo

AF:

0.296

Asia WGS

AF:

0.257

AC:

892

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.3

DANN

Benign

0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over