rs8103033

Variant names:

• chr19-39679413-G-A
• rs8103033
• ENST00000458539.5:n.21G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-39679413-G-A
• chr19-39679413-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458539.5(LGALS17A):​n.21G>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 ENST00000458539.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 18 publications found

Genes affected

LGALS17A (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LGALS17A	NR_034156.1	n.40G>A		non_coding_transcript_exon_variant	Exon 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS17A	ENST00000458539.5	n.21G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
LGALS17A	ENST00000598304.5	n.21G>A		non_coding_transcript_exon_variant	Exon 1 of 3	1
LGALS17A	ENST00000598736.5	n.21G>A		non_coding_transcript_exon_variant	Exon 1 of 8	1

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

African (AFR) AF: 0.200 AC: 16 AN: 80

American (AMR) AF: 0.667 AC: 8 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.191 AC: 18 AN: 94

European-Finnish (FIN) AF: 0.365 AC: 5763 AN: 15808

Middle Eastern (MID) AF: 0.248 AC: 405 AN: 1632

European-Non Finnish (NFE) AF: 0.335 AC: 93 AN: 278

Other (OTH) AF: 0.271 AC: 79 AN: 292

GnomAD4 genome AF: 0.288 AC: 43830 AN: 152102 Hom.: 7290 Cov.: 32 AF XY: 0.289 AC XY: 21508 AN XY: 74346

African (AFR) AF: 0.133 AC: 5509 AN: 41502

American (AMR) AF: 0.486 AC: 7415 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1568 AN: 5174

South Asian (SAS) AF: 0.199 AC: 958 AN: 4826

European-Finnish (FIN) AF: 0.366 AC: 3868 AN: 10568

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22221 AN: 67980

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.317 Hom.: 26811

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
PhyloP100		-0.017

Splicing

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

Other links and lift over

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