5-111647476-C-T

Variant names:

• chr5-111647476-C-T
• rs10515432
• ENST00000500779.2:n.284-21943C>T

Variant summary

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

The ENST00000500779.2(STARD4-AS1):​n.284-21943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,180 control chromosomes in the GnomAD database, including 762 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 0.064 (762 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.284-21943C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.284-21943C>T		intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1	n.2114-21943C>T		intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1	n.294-21943C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9652 AN: 152062 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0636 AC: 9683 AN: 152180 Hom.: 762 Cov.: 32 AF XY: 0.0639 AC XY: 4757 AN XY: 74426

African (AFR) AF: 0.174 AC: 7236 AN: 41490

American (AMR) AF: 0.0625 AC: 955 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5192

South Asian (SAS) AF: 0.0438 AC: 211 AN: 4822

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10584

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00450 AC: 306 AN: 68020

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

Alfa AF: 0.0429 Hom.: 69

Bravo AF: 0.0731

Asia WGS AF: 0.0970 AC: 338 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		-0.043
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: rs10515432; hg19: chr5-110983173;