rs152875

Positions:

• chr5-111516173-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105369177 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369177	XR_948671.3	n.589T>C		non_coding_transcript_exon_variant	1/4
STARD4-AS1	NR_040093.1	n.283+3665T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.283+3665T>C		intron_variant, non_coding_transcript_variant		1
STARD4-AS1	ENST00000666013.1	n.2113+3665T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.185

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs152875; hg19: chr5-110851871;