rs41275208

Variant names:

• chr12-21373509-C-A
• rs41275208
• NM_000415.3:c.80+78C>A

Variant summary

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

The NM_134431.5(SLCO1A2):​c.-63+890G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 947,318 control chromosomes in the GnomAD database, including 996 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 0.044 (160 hom., cov: 33)
  • Exomes 𝑓: 0.042 (836 hom.)
• Consequence: SLCO1A2 NM_134431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_134431.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IAPP	NM_000415.3	MANE Select	c.80+78C>A		intron	N/A	NP_000406.1
	SLCO1A2	NM_001386878.1		c.-63+29910G>T		intron	N/A	NP_001373807.1
	SLCO1A2	NM_001386881.1		c.-57-38805G>T		intron	N/A	NP_001373810.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IAPP	ENST00000240652.8	TSL:1 MANE Select	c.80+78C>A		intron	N/A	ENSP00000240652.3
	SLCO1A2	ENST00000307378.10	TSL:1	c.-63+890G>T		intron	N/A	ENSP00000305974.6
	SLCO1A2	ENST00000938257.1		c.-57-38805G>T		intron	N/A	ENSP00000608316.1

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6737 AN: 152122 Hom.: 160 Cov.: 33

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0371

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0569

GnomAD4 exome AF: 0.0424 AC: 33686 AN: 795078 Hom.: 836 Cov.: 10 AF XY: 0.0427 AC XY: 17996 AN XY: 421376

African (AFR) AF: 0.0573 AC: 1179 AN: 20590

American (AMR) AF: 0.0325 AC: 1398 AN: 43042

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 1266 AN: 21990

East Asian (EAS) AF: 0.0000549 AC: 2 AN: 36436

South Asian (SAS) AF: 0.0440 AC: 3181 AN: 72284

European-Finnish (FIN) AF: 0.0340 AC: 1698 AN: 49874

Middle Eastern (MID) AF: 0.0614 AC: 277 AN: 4514

European-Non Finnish (NFE) AF: 0.0452 AC: 22938 AN: 507860

Other (OTH) AF: 0.0454 AC: 1747 AN: 38488

GnomAD4 genome AF: 0.0443 AC: 6743 AN: 152240 Hom.: 160 Cov.: 33 AF XY: 0.0427 AC XY: 3180 AN XY: 74424

African (AFR) AF: 0.0527 AC: 2190 AN: 41562

American (AMR) AF: 0.0395 AC: 604 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4824

European-Finnish (FIN) AF: 0.0371 AC: 393 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3016 AN: 68006

Other (OTH) AF: 0.0559 AC: 118 AN: 2112

Alfa AF: 0.0116 Hom.: 6

Bravo AF: 0.0455

Asia WGS AF: 0.0180 AC: 64 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.56
PhyloP100		-0.070
PromoterAI		0.0051	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs41275208; hg19: chr12-21526443;