rs7981602

chr13-33487438-A-C

Variant summary

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

The ENST00000686875.1(ENSG00000230490):n.278+36800T>G 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 0.299 in 152,052 control chromosomes in the GnomAD database, including 7,644 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 (7644 hom., cov: 31)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

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 (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.30+36800T>G		intron_variant
STARD13	XM_017020835.3	c.30+36800T>G		intron_variant
STARD13	XM_024449429.2	c.30+36800T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686875.1	n.278+36800T>G		intron_variant, non_coding_transcript_variant
	ENST00000454681.2	n.226+36800T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45396 AN: 151934 Hom.: 7645 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.299 AC: 45394 AN: 152052 Hom.: 7644 Cov.: 31 AF XY: 0.294 AC XY: 21856 AN XY: 74310

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.320

Alfa AF: 0.334 Hom.: 1147

Bravo AF: 0.293

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7981602; hg19: chr13-34061575;