9-136441147-A-T

Variant names:

• chr9-136441147-A-T
• rs1127152
• NM_014866.2:c.*608T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014866.2(SEC16A):​c.*608T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: SEC16A NM_014866.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 37 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014866.2. 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
	SEC16A	NM_014866.2	MANE Select	c.*608T>A		3_prime_UTR	Exon 32 of 32	NP_055681.1	O15027-1
	SEC16A	NM_001438153.1		c.*608T>A		3_prime_UTR	Exon 31 of 31	NP_001425082.1
	SEC16A	NM_001438154.1		c.*608T>A		3_prime_UTR	Exon 31 of 31	NP_001425083.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC16A	ENST00000684901.1	MANE Select	c.*608T>A		3_prime_UTR	Exon 32 of 32	ENSP00000508822.1	O15027-1
	SEC16A	ENST00000290037.10	TSL:1	c.*608T>A		3_prime_UTR	Exon 29 of 29	ENSP00000290037.7	F1T0I1
	SEC16A	ENST00000453963.5	TSL:1	c.*608T>A		3_prime_UTR	Exon 26 of 26	ENSP00000403525.1	X6RGP5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.87
DANN	Benign	0.75
PhyloP100		0.093
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs1127152; hg19: chr9-139335599;