rs10515430

chr5-111603620-C-A

Variant summary

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

The NR_040093.1(STARD4-AS1):n.284-65799C>A variant causes a intron, non coding transcript 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 NR_040093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD4-AS1	NR_040093.1	n.284-65799C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.284-65799C>A		intron_variant, non_coding_transcript_variant		1
STARD4-AS1	ENST00000666013.1	n.2114-65799C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.0113

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.0325

Gnomad4 FIN AF: 0.00424

Gnomad4 NFE AF: 0.00930

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0310 Hom.: 38

Bravo AF: 0.0351

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515430; hg19: chr5-110939317;