rs10515430

Variant names:

• chr5-111603620-C-A
• rs10515430
• ENST00000500779.2:n.284-65799C>A

Variant summary

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

The ENST00000500779.2(STARD4-AS1):​n.284-65799C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 152,320 control chromosomes in the GnomAD database, including 124 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 0.029 (124 hom., cov: 33)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 1 publications found

Genes affected

STARD4-AS1 (HGNC:44117): (STARD4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500779.2. 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
	STARD4-AS1	NR_040093.1		n.284-65799C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	ENST00000500779.2	TSL:1	n.284-65799C>A		intron	N/A
	STARD4-AS1	ENST00000666013.1		n.2114-65799C>A		intron	N/A
	STARD4-AS1	ENST00000788272.1		n.294-65799C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0286 AC: 4347 AN: 152202 Hom.: 123 Cov.: 33

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00930

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0285 AC: 4348 AN: 152320 Hom.: 124 Cov.: 33 AF XY: 0.0301 AC XY: 2245 AN XY: 74482

African (AFR) AF: 0.0368 AC: 1530 AN: 41564

American (AMR) AF: 0.0962 AC: 1471 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3466

East Asian (EAS) AF: 0.0745 AC: 387 AN: 5194

South Asian (SAS) AF: 0.0325 AC: 157 AN: 4826

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00930 AC: 633 AN: 68036

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0318 Hom.: 38

Bravo AF: 0.0351

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		-0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10515430;

hg19: chr5-110939317;