rs9420790

Variant names:

• chr10-100496440-G-A
• rs9420790
• NM_015490.4:c.2137-9C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-100496440-G-A
• chr10-100496440-G-T

Variant summary

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

The NM_015490.4(SEC31B):​c.2137-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00464 in 1,613,870 control chromosomes in the GnomAD database, including 263 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 0.023 (152 hom., cov: 32)
  • Exomes 𝑓: 0.0027 (111 hom.)
• Consequence: SEC31B NM_015490.4 intron
• Scores: Splicing: ADA: 0.00001664
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

SEC31B (HGNC:23197): (SEC31 homolog B, COPII coat complex component) This gene encodes a protein of unknown function. The protein has moderate similarity to rat VAP1 protein which is an endosomal membrane-associated protein, containing a putative Ca2+/calmodulin-dependent kinase II phosphorylation site. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC31B	NM_015490.4	c.2137-9C>T		intron_variant	Intron 17 of 25	ENST00000370345.8	NP_056305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC31B	ENST00000370345.8	c.2137-9C>T		intron_variant	Intron 17 of 25	1	NM_015490.4	ENSP00000359370.3

Frequencies

GnomAD3 genomes AF: 0.0229 AC: 3492 AN: 152166 Hom.: 150 Cov.: 32

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000573

Gnomad OTH AF: 0.0187

GnomAD3 exomes AF: 0.00631 AC: 1582 AN: 250734 Hom.: 47 AF XY: 0.00467 AC XY: 633 AN XY: 135442

Gnomad AFR exome AF: 0.0802

Gnomad AMR exome AF: 0.00518

Gnomad ASJ exome AF: 0.000299

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000618

Gnomad OTH exome AF: 0.00376

GnomAD4 exome AF: 0.00272 AC: 3978 AN: 1461586 Hom.: 111 Cov.: 31 AF XY: 0.00236 AC XY: 1716 AN XY: 727088

Gnomad4 AFR exome AF: 0.0779

Gnomad4 AMR exome AF: 0.00597

Gnomad4 ASJ exome AF: 0.000192

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000162

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.000553

Gnomad4 OTH exome AF: 0.00704

GnomAD4 genome AF: 0.0231 AC: 3513 AN: 152284 Hom.: 152 Cov.: 32 AF XY: 0.0224 AC XY: 1665 AN XY: 74468

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.0111

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000559

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0109 Hom.: 31

Bravo AF: 0.0266

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000017
dbscSNV1_RF	Benign	0.0080
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: rs9420790; hg19: chr10-102256197;