12-21373538-A-G

Variant summary

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

The NM_000415.3(IAPP):c.80+107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 787,868 control chromosomes in the GnomAD database, including 22,229 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 (8682 hom., cov: 33)
  • Exomes 𝑓: 0.19 (13547 hom.)
• Consequence: IAPP NM_000415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

IAPP (HGNC:5329): (islet amyloid polypeptide) This gene encodes a member of the calcitonin family of peptide hormones. This hormone is released from pancreatic beta cells following food intake to regulate blood glucose levels and act as a satiation signal. Human patients with type 1 and advanced type 2 diabetes exhibit reduced levels of the encoded hormone in blood and pancreas. This protein also exhibits a bactericidal, antimicrobial activity. [provided by RefSeq, Jul 2016]

SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IAPP	NM_000415.3	c.80+107A>G		intron_variant		ENST00000240652.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IAPP	ENST00000240652.8	c.80+107A>G		intron_variant		1	NM_000415.3	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44005 AN: 152002 Hom.: 8649 Cov.: 33

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.193 AC: 122393 AN: 635748 Hom.: 13547 Cov.: 8 AF XY: 0.190 AC XY: 65017 AN XY: 342764

Gnomad4 AFR exome AF: 0.576

Gnomad4 AMR exome AF: 0.123

Gnomad4 ASJ exome AF: 0.251

Gnomad4 EAS exome AF: 0.145

Gnomad4 SAS exome AF: 0.161

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.290 AC: 44082 AN: 152120 Hom.: 8682 Cov.: 33 AF XY: 0.282 AC XY: 20933 AN XY: 74356

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.268

Alfa AF: 0.210 Hom.: 2445

Bravo AF: 0.305

Asia WGS AF: 0.179 AC: 624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.75
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12306121; hg19: chr12-21526472; COSMIC: COSV53713266;