rs9538078

Variant names:

• chr13-58502596-C-G
• rs9538078
• ENST00000784591.1:n.705-4417C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784591.1(ENSG00000302133):​n.705-4417C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,138 control chromosomes in the GnomAD database, including 2,479 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 0.16 (2479 hom., cov: 32)
• Consequence: ENSG00000302133 ENST00000784591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 1 publications found

Genes affected

ENSG00000302133 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302133	ENST00000784591.1	n.705-4417C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24491 AN: 152020 Hom.: 2480 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.161 AC: 24486 AN: 152138 Hom.: 2479 Cov.: 32 AF XY: 0.161 AC XY: 12001 AN XY: 74354

African (AFR) AF: 0.0428 AC: 1778 AN: 41516

American (AMR) AF: 0.163 AC: 2494 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.154 AC: 795 AN: 5160

South Asian (SAS) AF: 0.204 AC: 983 AN: 4818

European-Finnish (FIN) AF: 0.202 AC: 2134 AN: 10560

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14701 AN: 68006

Other (OTH) AF: 0.196 AC: 414 AN: 2112

Alfa AF: 0.180 Hom.: 359

Bravo AF: 0.153

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.49
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9538078; hg19: chr13-59076730; COSMIC: COSV69617982;