rs7731999

chr5-111603693-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040093.1(STARD4-AS1):n.284-65726T>C variant causes a intron, non coding transcript 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 NR_040093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD4-AS1	NR_040093.1	n.284-65726T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.284-65726T>C		intron_variant, non_coding_transcript_variant		1
STARD4-AS1	ENST00000666013.1	n.2114-65726T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.194

Alfa AF: 0.204 Hom.: 5805

Bravo AF: 0.208

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.5
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7731999; hg19: chr5-110939390;