ENST00000500779.2:n.284-50288G>A

Variant names:

• chr5-111619131-G-A
• rs2043833
• ENST00000500779.2:n.284-50288G>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.284-50288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,042 control chromosomes in the GnomAD database, including 3,366 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 0.21 (3366 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.284-50288G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.284-50288G>A		intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1	n.2114-50288G>A		intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1	n.294-50288G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31889 AN: 151924 Hom.: 3361 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.210 AC: 31925 AN: 152042 Hom.: 3366 Cov.: 32 AF XY: 0.210 AC XY: 15598 AN XY: 74324

African (AFR) AF: 0.205 AC: 8493 AN: 41466

American (AMR) AF: 0.266 AC: 4070 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1133 AN: 5174

South Asian (SAS) AF: 0.132 AC: 635 AN: 4818

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10560

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14109 AN: 67956

Other (OTH) AF: 0.198 AC: 418 AN: 2106

Alfa AF: 0.185 Hom.: 1455

Bravo AF: 0.216

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.49
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2043833; hg19: chr5-110954828;