rs2236711

Variant names:

• chr11-130869389-G-A
• rs2236711
• NM_014758.3:c.*9033C>T

Variant summary

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

The NM_014758.3(SNX19):​c.*9033C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,064 control chromosomes in the GnomAD database, including 14,825 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 0.44 (14825 hom., cov: 34)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SNX19 NM_014758.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 8 publications found

Genes affected

SNX19 (HGNC:21532): (sorting nexin 19) Islet antigen-2 (IA-2) is an autoantigen in type 1 diabetes and plays a role in insulin secretion. IA-2 is found in dense-core secretory vesicles and interacts with the product of this gene, a sorting nexin. In mouse pancreatic beta-cells, the encoded protein influenced insulin secretion by stabilizing the number of dense-core secretory vesicles. [provided by RefSeq, Dec 2016]

ENSG00000255455 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014758.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX19	NM_014758.3	MANE Select	c.*9033C>T		3_prime_UTR	Exon 11 of 11	NP_055573.3
	SNX19	NR_144939.2		n.12637C>T		non_coding_transcript_exon	Exon 12 of 12
	SNX19	NM_001347918.2		c.*9033C>T		3_prime_UTR	Exon 10 of 10	NP_001334847.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX19	ENST00000265909.9	TSL:1 MANE Select	c.*9033C>T		3_prime_UTR	Exon 11 of 11	ENSP00000265909.4
	ENSG00000255455	ENST00000525716.2	TSL:6	n.859C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66485 AN: 151944 Hom.: 14827 Cov.: 34

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.437 AC: 66504 AN: 152062 Hom.: 14825 Cov.: 34 AF XY: 0.440 AC XY: 32695 AN XY: 74336

African (AFR) AF: 0.366 AC: 15151 AN: 41446

American (AMR) AF: 0.501 AC: 7650 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2371 AN: 5174

South Asian (SAS) AF: 0.561 AC: 2707 AN: 4824

European-Finnish (FIN) AF: 0.437 AC: 4614 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31085 AN: 67982

Other (OTH) AF: 0.423 AC: 894 AN: 2112

Alfa AF: 0.460 Hom.: 8545

Bravo AF: 0.437

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2236711; hg19: chr11-130739284;