rs1127152

Positions:

• chr9-136441147-A-G
• chr9-136441147-A-T

Variant summary

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

The NM_014866.2(SEC16A):​c.*608T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,994 control chromosomes in the GnomAD database, including 10,934 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 0.36 (10855 hom., cov: 33)
  • Exomes 𝑓: 0.43 (79 hom.)
• Consequence: SEC16A NM_014866.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

SEC16A (HGNC:29006): (SEC16 homolog A, endoplasmic reticulum export factor) This gene encodes a protein that forms part of the Sec16 complex. This protein has a role in protein transport from the endoplasmic reticulum (ER) to the Golgi and mediates COPII vesicle formation at the transitional ER. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Feb 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC16A	NM_014866.2	c.*608T>C		3_prime_UTR_variant	32/32	ENST00000684901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC16A	ENST00000684901.1	c.*608T>C		3_prime_UTR_variant	32/32		NM_014866.2	A2

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55321 AN: 152022 Hom.: 10836 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.433 AC: 370 AN: 854 Hom.: 79 Cov.: 0 AF XY: 0.428 AC XY: 189 AN XY: 442

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.529

Gnomad4 EAS exome AF: 0.436

Gnomad4 SAS exome AF: 0.261

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.432

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.364 AC: 55376 AN: 152140 Hom.: 10855 Cov.: 33 AF XY: 0.359 AC XY: 26692 AN XY: 74374

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.392

Alfa AF: 0.425 Hom.: 18364

Bravo AF: 0.373

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.55

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: rs1127152; hg19: chr9-139335599;