chr13-33461723-T-A

Position:

• chr13-33461723-T-A

Variant summary

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

The ENST00000686875.1(ENSG00000230490):​n.279-21999A>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 0.301 in 152,030 control chromosomes in the GnomAD database, including 7,632 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 0.30 (7632 hom., cov: 32)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD13	NM_001243476.3	c.31-21999A>T		intron_variant
STARD13	XM_017020835.3	c.31-21999A>T		intron_variant
STARD13	XM_024449429.2	c.31-21999A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686875.1	n.279-21999A>T		intron_variant, non_coding_transcript_variant
	ENST00000454681.2	n.227-21999A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45755 AN: 151912 Hom.: 7634 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.301 AC: 45767 AN: 152030 Hom.: 7632 Cov.: 32 AF XY: 0.296 AC XY: 21967 AN XY: 74304

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.316

Alfa AF: 0.336 Hom.: 1148

Bravo AF: 0.297

Asia WGS AF: 0.234 AC: 815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943110; hg19: chr13-34035860;