rs9578484

Variant names:

• chr13-22648951-A-G
• rs9578484
• ENST00000815334.1:n.746-1283T>C

Variant summary

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

The ENST00000815334.1(ENSG00000306102):​n.746-1283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,142 control chromosomes in the GnomAD database, including 3,663 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 0.21 (3663 hom., cov: 33)
• Consequence: ENSG00000306102 ENST00000815334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 2 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306102	ENST00000815334.1		n.746-1283T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31766 AN: 152024 Hom.: 3660 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.209 AC: 31791 AN: 152142 Hom.: 3663 Cov.: 33 AF XY: 0.211 AC XY: 15689 AN XY: 74360

African (AFR) AF: 0.307 AC: 12752 AN: 41486

American (AMR) AF: 0.186 AC: 2835 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3470

East Asian (EAS) AF: 0.191 AC: 988 AN: 5178

South Asian (SAS) AF: 0.122 AC: 589 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2597 AN: 10582

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11058 AN: 68008

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.170 Hom.: 4076

Bravo AF: 0.208

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.29
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9578484;

hg19: chr13-23223090;