rs10240718

Variant names:

• chr7-38190936-C-T
• rs10240718
• NM_032016.4:c.-59+12516C>T

Variant summary

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

The NM_032016.4(STARD3NL):​c.-59+12516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 152,154 control chromosomes in the GnomAD database, including 565 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 0.081 (565 hom., cov: 33)
• Consequence: STARD3NL NM_032016.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032016.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD3NL	NM_032016.4	MANE Select	c.-59+12516C>T		intron	N/A	NP_114405.1
	STARD3NL	NM_001363339.2		c.-311-10778C>T		intron	N/A	NP_001350268.1
	STARD3NL	NM_001363340.2		c.-59+11791C>T		intron	N/A	NP_001350269.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD3NL	ENST00000009041.12	TSL:1 MANE Select	c.-59+12516C>T		intron	N/A	ENSP00000009041.7
	STARD3NL	ENST00000881125.1		c.-59+12516C>T		intron	N/A	ENSP00000551184.1
	STARD3NL	ENST00000396013.5	TSL:5	c.-59+11791C>T		intron	N/A	ENSP00000379334.1

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12373 AN: 152036 Hom.: 564 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0814 AC: 12386 AN: 152154 Hom.: 565 Cov.: 33 AF XY: 0.0774 AC XY: 5760 AN XY: 74396

African (AFR) AF: 0.102 AC: 4220 AN: 41506

American (AMR) AF: 0.0651 AC: 996 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4822

European-Finnish (FIN) AF: 0.0438 AC: 463 AN: 10572

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0867 AC: 5895 AN: 67994

Other (OTH) AF: 0.0886 AC: 187 AN: 2110

Alfa AF: 0.0878 Hom.: 238

Bravo AF: 0.0881

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		0.17
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: rs10240718; hg19: chr7-38230538;