rs10489882

Positions:

• chr1-177935360-T-C

Variant summary

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

The NM_033127.4(SEC16B):​c.2571+938A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,008 control chromosomes in the GnomAD database, including 10,092 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 0.35 (10092 hom., cov: 32)
• Consequence: SEC16B NM_033127.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

Genes affected

SEC16B (HGNC:30301): (SEC16 homolog B, endoplasmic reticulum export factor) SEC16B is a mammalian homolog of S. cerevisiae Sec16 that is required for organization of transitional endoplasmic reticulum (ER) sites and protein export (Bhattacharyya and Glick, 2007 [PubMed 17192411]).[supplied by OMIM, Jun 2009]

CRYZL2P-SEC16B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC16B	NM_033127.4	c.2571+938A>G		intron_variant		ENST00000308284.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC16B	ENST00000308284.11	c.2571+938A>G		intron_variant		1	NM_033127.4	A2
SEC16B	ENST00000528461.5	c.*1558+938A>G		intron_variant, NMD_transcript_variant		1
SEC16B	ENST00000327037.8	n.1281+938A>G		intron_variant, non_coding_transcript_variant		2
SEC16B	ENST00000495165.5	n.69+938A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53760 AN: 151890 Hom.: 10092 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.409

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53765 AN: 152008 Hom.: 10092 Cov.: 32 AF XY: 0.352 AC XY: 26175 AN XY: 74290

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.408

Alfa AF: 0.411 Hom.: 17714

Bravo AF: 0.347

Asia WGS AF: 0.271 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.24

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: rs10489882; hg19: chr1-177904495;