2-96195421-C-G

Position:

• chr2-96195421-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020151.4(STARD7):​c.419G>C​(p.Arg140Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,610,920 control chromosomes in the GnomAD database, including 22,112 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.14 (1591 hom., cov: 32)
  • Exomes 𝑓: 0.16 (20521 hom.)
• Consequence: STARD7 NM_020151.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15

Genes affected

STARD7 (HGNC:18063): (StAR related lipid transfer domain containing 7) Predicted to enable lipid binding activity. Predicted to act upstream of or within several processes, including establishment of skin barrier; mucociliary clearance; and myeloid dendritic cell activation. Predicted to be located in cytoplasm and extracellular region. Implicated in familial adult myoclonic epilepsy 2. [provided by Alliance of Genome Resources, Apr 2022]

STARD7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0013928711).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD7	NM_020151.4	c.419G>C	p.Arg140Pro	missense_variant	2/8	ENST00000337288.10	NP_064536.2
STARD7	NM_001385622.1	c.116G>C	p.Arg39Pro	missense_variant	2/8		NP_001372551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD7	ENST00000337288.10	c.419G>C	p.Arg140Pro	missense_variant	2/8	1	NM_020151.4	ENSP00000338030.5
STARD7	ENST00000443962.1	c.116G>C	p.Arg39Pro	missense_variant	2/5	5		ENSP00000409410.1
STARD7	ENST00000462501.1	n.94G>C		non_coding_transcript_exon_variant	1/7	2
STARD7	ENST00000488084.1	n.166G>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20563 AN: 152116 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.166

GnomAD3 exomes AF: 0.151 AC: 37184 AN: 246030 Hom.: 3128 AF XY: 0.157 AC XY: 20859 AN XY: 132892

Gnomad AFR exome AF: 0.0585

Gnomad AMR exome AF: 0.117

Gnomad ASJ exome AF: 0.157

Gnomad EAS exome AF: 0.108

Gnomad SAS exome AF: 0.224

Gnomad FIN exome AF: 0.147

Gnomad NFE exome AF: 0.161

Gnomad OTH exome AF: 0.176

GnomAD4 exome AF: 0.163 AC: 238489 AN: 1458686 Hom.: 20521 Cov.: 33 AF XY: 0.166 AC XY: 120597 AN XY: 725306

Gnomad4 AFR exome AF: 0.0636

Gnomad4 AMR exome AF: 0.121

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.228

Gnomad4 FIN exome AF: 0.146

Gnomad4 NFE exome AF: 0.165

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.135 AC: 20590 AN: 152234 Hom.: 1591 Cov.: 32 AF XY: 0.137 AC XY: 10166 AN XY: 74414

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.170

Alfa AF: 0.149 Hom.: 1453

Bravo AF: 0.128

TwinsUK AF: 0.171 AC: 635

ALSPAC AF: 0.160 AC: 615

ESP6500AA AF: 0.0667 AC: 294

ESP6500EA AF: 0.165 AC: 1418

ExAC AF: 0.149 AC: 18115

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.60	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.65
DEOGEN2	Benign	0.0055	T;T
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.62
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.071	T;T
MetaRNN	Benign	0.0014	T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	-0.97	N;.
PrimateAI	Benign	0.45	T
PROVEAN	Benign	1.7	N;N
REVEL	Uncertain	0.32
Sift	Benign	1.0	T;T
Sift4G	Benign	0.77	T;.
Polyphen		0.0	B;.
Vest4		0.043
MPC		0.82
ClinPred		0.0098	T
GERP RS		4.7
Varity_R		0.11
gMVP		0.40

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

Other links and lift over

dbSNP: rs2276650; hg19: chr2-96861159; COSMIC: COSV61525305; COSMIC: COSV61525305;