chr7-38228794-C-T

Variant summary

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

The NM_032016.4(STARD3NL):​c.650-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 1,605,086 control chromosomes in the GnomAD database, including 169,010 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14251 hom., cov: 33)
Exomes 𝑓: 0.46 ( 154759 hom. )

Consequence

STARD3NL
NM_032016.4 splice_region, intron

Scores

2
Splicing: ADA: 0.00002361
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.136
Variant links:
Genes affected
STARD3NL (HGNC:19169): (STARD3 N-terminal like) This gene encodes a late-endosomal protein that contains a conserved MENTAL (MLN64 N-terminal) domain. The encoded protein binds cholesterol molecules and may play a role in endosomal cholesterol transport through interactions with metastatic lymph node protein 64 (MLN64). [provided by RefSeq, Sep 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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STARD3NLNM_032016.4 linkc.650-5C>T splice_region_variant, intron_variant Intron 7 of 8 ENST00000009041.12 NP_114405.1 O95772-1A0A024RA89

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STARD3NLENST00000009041.12 linkc.650-5C>T splice_region_variant, intron_variant Intron 7 of 8 1 NM_032016.4 ENSP00000009041.7 O95772-1
STARD3NLENST00000396013.5 linkc.650-5C>T splice_region_variant, intron_variant Intron 8 of 9 5 ENSP00000379334.1 O95772-1
STARD3NLENST00000434197.5 linkc.596-5C>T splice_region_variant, intron_variant Intron 6 of 7 5 ENSP00000394000.1 C9JKL2
STARD3NLENST00000471550.1 linkn.2833-5C>T splice_region_variant, intron_variant Intron 5 of 6 2

Frequencies

GnomAD3 genomes
AF:
0.428
AC:
65048
AN:
151900
Hom.:
14241
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.338
Gnomad AMI
AF:
0.312
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.502
Gnomad EAS
AF:
0.495
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.423
GnomAD3 exomes
AF:
0.464
AC:
116183
AN:
250476
Hom.:
27336
AF XY:
0.463
AC XY:
62671
AN XY:
135436
show subpopulations
Gnomad AFR exome
AF:
0.337
Gnomad AMR exome
AF:
0.532
Gnomad ASJ exome
AF:
0.492
Gnomad EAS exome
AF:
0.472
Gnomad SAS exome
AF:
0.485
Gnomad FIN exome
AF:
0.451
Gnomad NFE exome
AF:
0.455
Gnomad OTH exome
AF:
0.446
GnomAD4 exome
AF:
0.459
AC:
666647
AN:
1453068
Hom.:
154759
Cov.:
31
AF XY:
0.459
AC XY:
332250
AN XY:
723164
show subpopulations
Gnomad4 AFR exome
AF:
0.336
Gnomad4 AMR exome
AF:
0.525
Gnomad4 ASJ exome
AF:
0.493
Gnomad4 EAS exome
AF:
0.546
Gnomad4 SAS exome
AF:
0.487
Gnomad4 FIN exome
AF:
0.451
Gnomad4 NFE exome
AF:
0.455
Gnomad4 OTH exome
AF:
0.451
GnomAD4 genome
AF:
0.428
AC:
65099
AN:
152018
Hom.:
14251
Cov.:
33
AF XY:
0.433
AC XY:
32160
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.494
Gnomad4 ASJ
AF:
0.502
Gnomad4 EAS
AF:
0.496
Gnomad4 SAS
AF:
0.480
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.454
Gnomad4 OTH
AF:
0.421
Alfa
AF:
0.446
Hom.:
18695
Bravo
AF:
0.424
Asia WGS
AF:
0.438
AC:
1522
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.57
DANN
Benign
0.24
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000024
dbscSNV1_RF
Benign
0.0
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: rs7795499; hg19: chr7-38268395; COSMIC: COSV50518278; API