rs251133

Variant names:

• chr5-111523548-G-A
• rs251133
• ENST00000500779.2:n.283+11040G>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+11040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,936 control chromosomes in the GnomAD database, including 10,105 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 0.31 (10105 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.283+11040G>A		intron_variant	Intron 1 of 6
LOC105369177	XR_001742458.2	n.385-1196G>A		intron_variant	Intron 1 of 2
LOC105369177	XR_948671.3	n.2264-1196G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.283+11040G>A		intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1	n.2113+11040G>A		intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1	n.293+11040G>A		intron_variant	Intron 1 of 5
ENSG00000302663	ENST00000788598.1	n.138-1203G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47345 AN: 151816 Hom.: 10079 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.312 AC: 47427 AN: 151936 Hom.: 10105 Cov.: 32 AF XY: 0.310 AC XY: 23021 AN XY: 74268

African (AFR) AF: 0.608 AC: 25144 AN: 41386

American (AMR) AF: 0.246 AC: 3759 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.180 AC: 929 AN: 5152

South Asian (SAS) AF: 0.137 AC: 659 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2551 AN: 10560

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13221 AN: 67968

Other (OTH) AF: 0.286 AC: 602 AN: 2102

Alfa AF: 0.223 Hom.: 18987

Bravo AF: 0.326

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs251133; hg19: chr5-110859246;