rs9569991

Positions:

• chr13-33649608-G-A
• chr13-33649608-G-T

Variant summary

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

The ENST00000686875.1(ENSG00000230490):​n.143+27070C>T 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 0.1 in 152,118 control chromosomes in the GnomAD database, including 1,667 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 0.10 (1667 hom., cov: 31)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.-106+11669C>T		intron_variant			NP_001230405.1
STARD13	XM_017020835.3	c.-106+27070C>T		intron_variant			XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686875.1	n.143+27070C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 15180 AN: 151998 Hom.: 1661 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.100 AC: 15222 AN: 152118 Hom.: 1667 Cov.: 31 AF XY: 0.101 AC XY: 7538 AN XY: 74376

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.00721

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.0339 Hom.: 661

Bravo AF: 0.123

Asia WGS AF: 0.118 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9569991; hg19: chr13-34223745;