Variant 10-119909144-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007190.4(SEC23IP):c.1191+14T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 1,553,532 control chromosomes in the GnomAD database, including 5,982 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 0.054 ( 421 hom., cov: 32)

Exomes 𝑓: 0.069 ( 5561 hom. )

Consequence

SEC23IP
NM_007190.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.492

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 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.1191+14T>G		intron_variant		ENST00000369075.8	NP_009121.1	Q9Y6Y8-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SEC23IP	ENST00000369075.8 linkuse as main transcript	c.1191+14T>G	intron_variant	1	NM_007190.4	ENSP00000358071.3	Q9Y6Y8-1
SEC23IP	ENST00000705471.1 linkuse as main transcript	c.1191+14T>G	intron_variant			ENSP00000516127.1	A0A994J542
SEC23IP	ENST00000446561.1 linkuse as main transcript	c.304-2900T>G	intron_variant	3		ENSP00000396906.1	H7C0V8

Frequencies

GnomAD3 genomes

AF:

0.0544

AC:

8286

AN:

152188

Hom.:

421

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:

0.262

Gnomad FIN

AF:

0.0917

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0557

Gnomad OTH

AF:

0.0430

GnomAD3 exomes

AF:

0.0863

AC:

19374

AN:

224624

Hom.:

1414

AF XY:

0.0935

AC XY:

11386

AN XY:

121838

show subpopulations

Gnomad AFR exome

AF:

0.00950

Gnomad AMR exome

AF:

0.0479

Gnomad ASJ exome

AF:

0.0446

Gnomad EAS exome

AF:

0.188

Gnomad SAS exome

AF:

0.253

Gnomad FIN exome

AF:

0.0919

Gnomad NFE exome

AF:

0.0552

Gnomad OTH exome

AF:

0.0715

GnomAD4 exome

AF:

0.0693

AC:

97107

AN:

1401224

Hom.:

5561

Cov.:

AF XY:

0.0746

AC XY:

52185

AN XY:

699092

show subpopulations

Gnomad4 AFR exome

AF:

0.00919

Gnomad4 AMR exome

AF:

0.0421

Gnomad4 ASJ exome

AF:

0.0402

Gnomad4 EAS exome

AF:

0.194

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.0883

Gnomad4 NFE exome

AF:

0.0540

Gnomad4 OTH exome

AF:

0.0734

GnomAD4 genome

AF:

0.0544

AC:

8290

AN:

152308

Hom.:

421

Cov.:

AF XY:

0.0597

AC XY:

4446

AN XY:

74476

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:

0.262

Gnomad4 FIN

AF:

0.0917

Gnomad4 NFE

AF:

0.0557

Gnomad4 OTH

AF:

0.0444

Alfa

AF:

0.0376

Hom.:

Bravo

AF:

0.0440

Asia WGS

AF:

0.196

AC:

682

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.18

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over