NM_032016.4:c.-58-6140A>G

Variant names:

• chr7-38201307-A-G
• rs4723738
• NM_032016.4:c.-58-6140A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032016.4(STARD3NL):​c.-58-6140A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,986 control chromosomes in the GnomAD database, including 14,202 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 0.43 (14202 hom., cov: 32)
• Consequence: STARD3NL NM_032016.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD3NL	NM_032016.4	c.-58-6140A>G		intron_variant	Intron 1 of 8	ENST00000009041.12	NP_114405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD3NL	ENST00000009041.12	c.-58-6140A>G		intron_variant	Intron 1 of 8	1	NM_032016.4	ENSP00000009041.7

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64892 AN: 151870 Hom.: 14194 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.423

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.427 AC: 64941 AN: 151986 Hom.: 14202 Cov.: 32 AF XY: 0.432 AC XY: 32070 AN XY: 74282

African (AFR) AF: 0.335 AC: 13895 AN: 41476

American (AMR) AF: 0.492 AC: 7505 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2578 AN: 5182

South Asian (SAS) AF: 0.484 AC: 2329 AN: 4808

European-Finnish (FIN) AF: 0.450 AC: 4738 AN: 10530

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30871 AN: 67938

Other (OTH) AF: 0.421 AC: 891 AN: 2116

Alfa AF: 0.438 Hom.: 27143

Bravo AF: 0.423

Asia WGS AF: 0.441 AC: 1526 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4723738; hg19: chr7-38240908;