5-111524099-G-A

Variant names:

• chr5-111524099-G-A
• rs251130
• ENST00000500779.2:n.283+11591G>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.283+11591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,014 control chromosomes in the GnomAD database, including 17,096 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 0.42 (17096 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 11 publications found

Genes affected

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

ENSG00000302663 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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.283+11591G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	ENST00000500779.2	TSL:1	n.283+11591G>A		intron	N/A
	STARD4-AS1	ENST00000666013.1		n.2113+11591G>A		intron	N/A
	STARD4-AS1	ENST00000788272.1		n.293+11591G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63559 AN: 151896 Hom.: 17038 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.419 AC: 63683 AN: 152014 Hom.: 17096 Cov.: 32 AF XY: 0.417 AC XY: 30965 AN XY: 74322

African (AFR) AF: 0.769 AC: 31898 AN: 41458

American (AMR) AF: 0.365 AC: 5575 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1295 AN: 5172

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4818

European-Finnish (FIN) AF: 0.313 AC: 3299 AN: 10544

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18663 AN: 67968

Other (OTH) AF: 0.378 AC: 796 AN: 2104

Alfa AF: 0.318 Hom.: 14031

Bravo AF: 0.439

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		0.030

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: rs251130;

hg19: chr5-110859797;