5-111603693-T-C

Variant names:

• chr5-111603693-T-C
• rs7731999
• ENST00000500779.2:n.284-65726T>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.284-65726T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,198 control chromosomes in the GnomAD database, including 3,181 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 0.20 (3181 hom., cov: 33)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500779.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	NR_040093.1		n.284-65726T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	ENST00000500779.2	TSL:1	n.284-65726T>C		intron	N/A
	STARD4-AS1	ENST00000666013.1		n.2114-65726T>C		intron	N/A
	STARD4-AS1	ENST00000788272.1		n.294-65726T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30836 AN: 152080 Hom.: 3174 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.203 AC: 30887 AN: 152198 Hom.: 3181 Cov.: 33 AF XY: 0.203 AC XY: 15106 AN XY: 74412

African (AFR) AF: 0.182 AC: 7566 AN: 41542

American (AMR) AF: 0.263 AC: 4017 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5176

South Asian (SAS) AF: 0.132 AC: 637 AN: 4830

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10594

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14038 AN: 67988

Other (OTH) AF: 0.194 AC: 410 AN: 2110

Alfa AF: 0.206 Hom.: 12769

Bravo AF: 0.208

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7731999; hg19: chr5-110939390;