rs8103033

chr19-39679413-G-Achr19-39679413-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

LGALS17A (HGNC:):

ACMG classification

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	UniProt
LGALS17A	NR_034156.1	n.40G>A		non_coding_transcript_exon_variant	1/8

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43802 AN: 151984 Hom.: 7278 Cov.: 32

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.: 0 AF XY: 0.350 AC XY: 3052 AN XY: 8716

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.: 32 AF XY: 0.289 AC XY: 21508 AN XY: 74346

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

Other links and lift over

dbSNP: rs8103033; hg19: chr19-40170053; COSMIC: COSV69664251;