Variant 10-119912139-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_007190.4(SEC23IP):c.1287T>C(p.Asp429Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.069 in 1,613,904 control chromosomes in the GnomAD database, including 6,496 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.055 ( 431 hom., cov: 32)

Exomes 𝑓: 0.071 ( 6065 hom. )

Consequence

SEC23IP
NM_007190.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0180

Variant links:

Genes affected

SEC23IP (HGNC:17018): (SEC23 interacting protein) This gene encodes a member of the phosphatidic acid preferring-phospholipase A1 family. The encoded protein is localized to endoplasmic reticulum exit sites and plays a critical role in ER-Golgi transport as part of the multimeric coat protein II complex. An orthologous gene in frogs is required for normal neural crest cell development, suggesting that this gene may play a role in Waardenburg syndrome neural crest defects. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]

SEC23IP links:

SEC23IP (HGNC:):

SEC23IP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 10-119912139-T-C is Benign according to our data. Variant chr10-119912139-T-C is described in ClinVar as [Benign]. Clinvar id is 3055672.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.018 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEC23IP	NM_007190.4 linkuse as main transcript	c.1287T>C	p.Asp429Asp	synonymous_variant	6/19	ENST00000369075.8	NP_009121.1	Q9Y6Y8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SEC23IP	ENST00000369075.8 linkuse as main transcript	c.1287T>C	p.Asp429Asp	synonymous_variant	6/19	1	NM_007190.4	ENSP00000358071.3	Q9Y6Y8-1
SEC23IP	ENST00000705471.1 linkuse as main transcript	c.1287T>C	p.Asp429Asp	synonymous_variant	6/19			ENSP00000516127.1	A0A994J542
SEC23IP	ENST00000446561.1 linkuse as main transcript	c.399T>C	p.Asp133Asp	synonymous_variant	3/5	3		ENSP00000396906.1	H7C0V8

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8317

AN:

152128

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.0769

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.0378

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.0916

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0557

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0889

AC:

22358

AN:

251358

Hom.:

1723

AF XY:

0.0977

AC XY:

13269

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.00947

Gnomad AMR exome

AF:

0.0490

Gnomad ASJ exome

AF:

0.0445

Gnomad EAS exome

AF:

0.187

Gnomad SAS exome

AF:

0.257

Gnomad FIN exome

AF:

0.0925

Gnomad NFE exome

AF:

0.0555

Gnomad OTH exome

AF:

0.0721

GnomAD4 exome

AF:

0.0705

AC:

103073

AN:

1461658

Hom.:

6065

Cov.:

AF XY:

0.0763

AC XY:

55508

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.00956

Gnomad4 AMR exome

AF:

0.0461

Gnomad4 ASJ exome

AF:

0.0408

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.252

Gnomad4 FIN exome

AF:

0.0886

Gnomad4 NFE exome

AF:

0.0544

Gnomad4 OTH exome

AF:

0.0749

GnomAD4 genome

AF:

0.0547

AC:

8323

AN:

152246

Hom.:

431

Cov.:

AF XY:

0.0600

AC XY:

4467

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0103

Gnomad4 AMR

AF:

0.0369

Gnomad4 ASJ

AF:

0.0378

Gnomad4 EAS

AF:

0.185

Gnomad4 SAS

AF:

0.270

Gnomad4 FIN

AF:

0.0916

Gnomad4 NFE

AF:

0.0557

Gnomad4 OTH

AF:

0.0449

Alfa

AF:

0.0512

Hom.:

199

Bravo

AF:

0.0441

Asia WGS

AF:

0.202

AC:

701

AN:

3478

EpiCase

AF:

0.0565

EpiControl

AF:

0.0555

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SEC23IP-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.3

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over