ENST00000500779.2:n.283+18044C>T

Variant names:

• chr5-111530552-C-T
• rs524203
• ENST00000500779.2:n.283+18044C>T

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+18044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,106 control chromosomes in the GnomAD database, including 4,966 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 0.23 (4966 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 2 publications found

Genes affected

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

ENSG00000302689 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.283+18044C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.283+18044C>T		intron_variant	Intron 1 of 6	1
ENSG00000302689	ENST00000788917.1	n.300G>A		non_coding_transcript_exon_variant	Exon 1 of 2
STARD4-AS1	ENST00000666013.1	n.2113+18044C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34219 AN: 151986 Hom.: 4963 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.225 AC: 34262 AN: 152106 Hom.: 4966 Cov.: 32 AF XY: 0.225 AC XY: 16702 AN XY: 74364

African (AFR) AF: 0.410 AC: 17009 AN: 41450

American (AMR) AF: 0.199 AC: 3039 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.145 AC: 750 AN: 5184

South Asian (SAS) AF: 0.126 AC: 607 AN: 4818

European-Finnish (FIN) AF: 0.184 AC: 1942 AN: 10578

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9993 AN: 67996

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.165 Hom.: 1902

Bravo AF: 0.235

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.78
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs524203; hg19: chr5-110866250;