rs152875

Variant names:

• chr5-111516173-T-C
• rs152875
• ENST00000500779.2:n.283+3665T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948671.3(LOC105369177):​n.589T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,074 control chromosomes in the GnomAD database, including 2,518 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 0.18 (2518 hom., cov: 32)
• Consequence: LOC105369177 XR_948671.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977
• Publications: 1 publications found

Genes affected

STARD4-AS1 (HGNC:44117): (STARD4 antisense RNA 1)

LOC105369177 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	NR_040093.1		n.283+3665T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	ENST00000500779.2	TSL:1	n.283+3665T>C		intron	N/A
	STARD4-AS1	ENST00000666013.1		n.2113+3665T>C		intron	N/A
	STARD4-AS1	ENST00000788272.1		n.293+3665T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26794 AN: 151956 Hom.: 2516 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.176 AC: 26817 AN: 152074 Hom.: 2518 Cov.: 32 AF XY: 0.177 AC XY: 13135 AN XY: 74338

African (AFR) AF: 0.236 AC: 9793 AN: 41488

American (AMR) AF: 0.183 AC: 2786 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3468

East Asian (EAS) AF: 0.147 AC: 760 AN: 5178

South Asian (SAS) AF: 0.127 AC: 612 AN: 4814

European-Finnish (FIN) AF: 0.184 AC: 1939 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10073 AN: 67982

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.161 Hom.: 283

Bravo AF: 0.178

Asia WGS AF: 0.138 AC: 482 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.86
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs152875; hg19: chr5-110851871;