5-111623085-G-A

Variant names:

• chr5-111623085-G-A
• rs11241130
• ENST00000500779.2:n.284-46334G>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.284-46334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,972 control chromosomes in the GnomAD database, including 50,531 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 0.80 (50531 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.284-46334G>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.284-46334G>A		intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1	n.2114-46334G>A		intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1	n.294-46334G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121182 AN: 151854 Hom.: 50516 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.798 AC: 121241 AN: 151972 Hom.: 50531 Cov.: 32 AF XY: 0.798 AC XY: 59305 AN XY: 74320

African (AFR) AF: 0.533 AC: 22043 AN: 41382

American (AMR) AF: 0.854 AC: 13046 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3009 AN: 3472

East Asian (EAS) AF: 0.798 AC: 4128 AN: 5176

South Asian (SAS) AF: 0.746 AC: 3597 AN: 4824

European-Finnish (FIN) AF: 0.927 AC: 9774 AN: 10542

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62795 AN: 67980

Other (OTH) AF: 0.806 AC: 1700 AN: 2110

Alfa AF: 0.871 Hom.: 123001

Bravo AF: 0.781

Asia WGS AF: 0.780 AC: 2697 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs11241130; hg19: chr5-110958782;