rs9315219

chr13-33488647-C-T

Variant summary

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

The ENST00000686875.1(ENSG00000230490):n.278+35591G>A 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 0.259 in 152,102 control chromosomes in the GnomAD database, including 6,289 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 0.26 (6289 hom., cov: 32)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD13	NM_001243476.3	c.30+35591G>A		intron_variant
STARD13	XM_017020835.3	c.30+35591G>A		intron_variant
STARD13	XM_024449429.2	c.30+35591G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686875.1	n.278+35591G>A		intron_variant, non_coding_transcript_variant
	ENST00000454681.2	n.226+35591G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39456 AN: 151984 Hom.: 6289 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.259 AC: 39451 AN: 152102 Hom.: 6289 Cov.: 32 AF XY: 0.257 AC XY: 19095 AN XY: 74370

Gnomad4 AFR AF: 0.0747

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.274

Alfa AF: 0.302 Hom.: 1017

Bravo AF: 0.251

Asia WGS AF: 0.237 AC: 822 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315219; hg19: chr13-34062784;