10-119920847-A-G

Variant summary

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

The NM_007190.4(SEC23IP):​c.2026-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 1,295,424 control chromosomes in the GnomAD database, including 5,537 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 0.055 ( 430 hom., cov: 33)
Exomes 𝑓: 0.072 ( 5107 hom. )

Consequence

SEC23IP
NM_007190.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.90
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]

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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=-0.85).
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 rank MANE Protein UniProt
SEC23IPNM_007190.4 linkc.2026-42A>G intron_variant Intron 11 of 18 ENST00000369075.8 NP_009121.1 Q9Y6Y8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEC23IPENST00000369075.8 linkc.2026-42A>G intron_variant Intron 11 of 18 1 NM_007190.4 ENSP00000358071.3 Q9Y6Y8-1
SEC23IPENST00000705471.1 linkc.2026-42A>G intron_variant Intron 11 of 18 ENSP00000516127.1 A0A994J542

Frequencies

GnomAD3 genomes
AF:
0.0547
AC:
8330
AN:
152196
Hom.:
430
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0105
Gnomad AMI
AF:
0.0768
Gnomad AMR
AF:
0.0368
Gnomad ASJ
AF:
0.0377
Gnomad EAS
AF:
0.184
Gnomad SAS
AF:
0.269
Gnomad FIN
AF:
0.0918
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0557
Gnomad OTH
AF:
0.0439
GnomAD3 exomes
AF:
0.0880
AC:
20105
AN:
228366
Hom.:
1542
AF XY:
0.0959
AC XY:
11847
AN XY:
123498
show subpopulations
Gnomad AFR exome
AF:
0.00943
Gnomad AMR exome
AF:
0.0494
Gnomad ASJ exome
AF:
0.0453
Gnomad EAS exome
AF:
0.188
Gnomad SAS exome
AF:
0.262
Gnomad FIN exome
AF:
0.0918
Gnomad NFE exome
AF:
0.0555
Gnomad OTH exome
AF:
0.0742
GnomAD4 exome
AF:
0.0723
AC:
82639
AN:
1143110
Hom.:
5107
Cov.:
14
AF XY:
0.0784
AC XY:
45560
AN XY:
581382
show subpopulations
Gnomad4 AFR exome
AF:
0.00980
Gnomad4 AMR exome
AF:
0.0455
Gnomad4 ASJ exome
AF:
0.0409
Gnomad4 EAS exome
AF:
0.194
Gnomad4 SAS exome
AF:
0.251
Gnomad4 FIN exome
AF:
0.0880
Gnomad4 NFE exome
AF:
0.0541
Gnomad4 OTH exome
AF:
0.0736
GnomAD4 genome
AF:
0.0547
AC:
8336
AN:
152314
Hom.:
430
Cov.:
33
AF XY:
0.0601
AC XY:
4476
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0105
Gnomad4 AMR
AF:
0.0370
Gnomad4 ASJ
AF:
0.0377
Gnomad4 EAS
AF:
0.185
Gnomad4 SAS
AF:
0.269
Gnomad4 FIN
AF:
0.0918
Gnomad4 NFE
AF:
0.0557
Gnomad4 OTH
AF:
0.0454
Alfa
AF:
0.0347
Hom.:
57
Bravo
AF:
0.0441
Asia WGS
AF:
0.201
AC:
698
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.0090
DANN
Benign
0.75

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.

Other links and lift over

dbSNP: rs2271123; hg19: chr10-121680359; COSMIC: COSV64830657; COSMIC: COSV64830657; API