13-30767298-G-A

Variant names:

• chr13-30767298-G-A
• rs4445746

Variant summary

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

The variant allele was found at a frequency of 0.246 in 151,936 control chromosomes in the GnomAD database, including 4,743 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 0.25 (4743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37343 AN: 151816 Hom.: 4749 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.246 AC: 37346 AN: 151936 Hom.: 4743 Cov.: 32 AF XY: 0.246 AC XY: 18260 AN XY: 74264

African (AFR) AF: 0.312 AC: 12937 AN: 41410

American (AMR) AF: 0.173 AC: 2638 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.184 AC: 954 AN: 5174

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2367 AN: 10540

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15433 AN: 67938

Other (OTH) AF: 0.233 AC: 493 AN: 2112

Alfa AF: 0.219 Hom.: 2348

Bravo AF: 0.242

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4445746; hg19: chr13-31341435;