rs7998352

chr13-33560672-C-Achr13-33560672-C-T

Variant summary

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

The ENST00000686875.1(ENSG00000230490):n.144-36300G>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 0.238 in 151,060 control chromosomes in the GnomAD database, including 5,393 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 0.24 (5393 hom., cov: 32)
• Consequence: ENST00000686875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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 (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723406	XR_007063750.1	n.85+5855C>A		intron_variant, non_coding_transcript_variant
STARD13	NM_001243476.3	c.-105-36300G>T		intron_variant
STARD13	XM_017020835.3	c.-105-36300G>T		intron_variant
LOC102723406	XR_001749811.2	n.68+5855C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686875.1	n.144-36300G>T		intron_variant, non_coding_transcript_variant
	ENST00000454681.2	n.92-36300G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35801 AN: 150942 Hom.: 5355 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.238 AC: 35893 AN: 151060 Hom.: 5393 Cov.: 32 AF XY: 0.236 AC XY: 17463 AN XY: 73868

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.245

Alfa AF: 0.185 Hom.: 2678

Bravo AF: 0.253

Asia WGS AF: 0.293 AC: 1017 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.62
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7998352; hg19: chr13-34134809;