chr5-111574957-G-C

Variant names:

• chr5-111574957-G-C
• rs382900
• ENST00000500779.2:n.283+62449G>C

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+62449G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 151,294 control chromosomes in the GnomAD database, including 783 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 0.072 (783 hom., cov: 31)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.283+62449G>C		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+62449G>C		intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1	n.2113+62449G>C		intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1	n.293+62449G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10820 AN: 151178 Hom.: 778 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0863

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.00782

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0716 AC: 10839 AN: 151294 Hom.: 783 Cov.: 31 AF XY: 0.0724 AC XY: 5352 AN XY: 73938

African (AFR) AF: 0.134 AC: 5467 AN: 40846

American (AMR) AF: 0.0790 AC: 1205 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0863 AC: 299 AN: 3464

East Asian (EAS) AF: 0.134 AC: 692 AN: 5150

South Asian (SAS) AF: 0.159 AC: 746 AN: 4686

European-Finnish (FIN) AF: 0.00782 AC: 83 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0317 AC: 2152 AN: 67962

Other (OTH) AF: 0.0761 AC: 160 AN: 2102

Alfa AF: 0.00560 Hom.: 2

Bravo AF: 0.0792

Asia WGS AF: 0.123 AC: 429 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.062
DANN	Benign	0.31
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs382900; hg19: chr5-110910654;