Variant chr7-38228794-C-T details in Genebe, Genetics Data Aggregator

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, splice polypyrimidine tract, 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, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00002361

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]

STARD3NL 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=-0.88).

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/exons	MANE	Protein	UniProt
STARD3NL	NM_032016.4 linkuse as main transcript	c.650-5C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000009041.12	NP_114405.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
STARD3NL	ENST00000009041.12 linkuse as main transcript	c.650-5C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_032016.4	ENSP00000009041	P1	O95772-1
STARD3NL	ENST00000396013.5 linkuse as main transcript	c.650-5C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5		ENSP00000379334	P1	O95772-1
STARD3NL	ENST00000434197.5 linkuse as main transcript	c.596-5C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5		ENSP00000394000
STARD3NL	ENST00000471550.1 linkuse as main transcript	n.2833-5C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65048

AN:

151900

Hom.:

14241

Cov.:

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.:

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.:

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.

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