chr13-33469613-C-T

Position:

• chr13-33469613-C-T

Variant summary

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

The ENST00000686875.1(ENSG00000230490):​n.279-29889G>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 0.313 in 151,782 control chromosomes in the GnomAD database, including 8,049 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 0.31 (8049 hom., cov: 32)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.31-29889G>A		intron_variant			NP_001230405.1
STARD13	XM_017020835.3	c.31-29889G>A		intron_variant			XP_016876324.1
STARD13	XM_024449429.2	c.31-29889G>A		intron_variant			XP_024305197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686875.1	n.279-29889G>A		intron_variant, non_coding_transcript_variant
	ENST00000454681.2	n.227-29889G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47571 AN: 151664 Hom.: 8048 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.313 AC: 47582 AN: 151782 Hom.: 8049 Cov.: 32 AF XY: 0.308 AC XY: 22861 AN XY: 74150

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.331

Alfa AF: 0.378 Hom.: 20648

Bravo AF: 0.310

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315215; hg19: chr13-34043750;