rs1661409

Positions:

• chr11-101904932-G-A
• chr11-101904932-G-T

Variant summary

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

The NM_178127.5(ANGPTL5):​c.346-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,552,014 control chromosomes in the GnomAD database, including 127,279 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 0.34 (9735 hom., cov: 32)
  • Exomes 𝑓: 0.40 (117544 hom.)
• Consequence: ANGPTL5 NM_178127.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

ANGPTL5 (HGNC:19705): (angiopoietin like 5) Predicted to be active in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANGPTL5	NM_178127.5	c.346-25C>T		intron_variant		ENST00000334289.7	NP_835228.2
ANGPTL5	XM_011542735.4	c.345+812C>T		intron_variant			XP_011541037.1
ANGPTL5	XM_017017466.3	c.241+2171C>T		intron_variant			XP_016872955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANGPTL5	ENST00000334289.7	c.346-25C>T		intron_variant		1	NM_178127.5	ENSP00000335255	P1
ANGPTL5	ENST00000534527.1	c.345+812C>T		intron_variant		3		ENSP00000433562

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52305 AN: 151856 Hom.: 9740 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.354

GnomAD3 exomes AF: 0.368 AC: 91045 AN: 247238 Hom.: 17642 AF XY: 0.375 AC XY: 50248 AN XY: 134106

Gnomad AFR exome AF: 0.205

Gnomad AMR exome AF: 0.265

Gnomad ASJ exome AF: 0.443

Gnomad EAS exome AF: 0.453

Gnomad SAS exome AF: 0.313

Gnomad FIN exome AF: 0.359

Gnomad NFE exome AF: 0.417

Gnomad OTH exome AF: 0.404

GnomAD4 exome AF: 0.404 AC: 566082 AN: 1400040 Hom.: 117544 Cov.: 23 AF XY: 0.404 AC XY: 283003 AN XY: 700300

Gnomad4 AFR exome AF: 0.209

Gnomad4 AMR exome AF: 0.270

Gnomad4 ASJ exome AF: 0.443

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.319

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.398

GnomAD4 genome AF: 0.344 AC: 52300 AN: 151974 Hom.: 9735 Cov.: 32 AF XY: 0.338 AC XY: 25069 AN XY: 74264

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.349

Alfa AF: 0.410 Hom.: 27192

Bravo AF: 0.335

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1661409; hg19: chr11-101775663;