chr5-111643461-T-C

Variant names:

• chr5-111643461-T-C
• rs1379552
• ENST00000500779.2:n.284-25958T>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.284-25958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,028 control chromosomes in the GnomAD database, including 5,912 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 0.27 (5912 hom., cov: 32)
• Consequence: STARD4-AS1 ENST00000500779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 6 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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.284-25958T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD4-AS1	ENST00000500779.2	TSL:1	n.284-25958T>C		intron	N/A
	STARD4-AS1	ENST00000666013.1		n.2114-25958T>C		intron	N/A
	STARD4-AS1	ENST00000788272.1		n.294-25958T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41410 AN: 151912 Hom.: 5886 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.273 AC: 41477 AN: 152028 Hom.: 5912 Cov.: 32 AF XY: 0.273 AC XY: 20288 AN XY: 74302

African (AFR) AF: 0.316 AC: 13111 AN: 41466

American (AMR) AF: 0.358 AC: 5473 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2192 AN: 5154

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4816

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15701 AN: 67948

Other (OTH) AF: 0.268 AC: 567 AN: 2116

Alfa AF: 0.248 Hom.: 3947

Bravo AF: 0.289

Asia WGS AF: 0.312 AC: 1083 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.85
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1379552;

hg19: chr5-110979158;