rs894363

Variant names:

• chr4-99455689-C-T
• rs894363

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 0.32 in 150,278 control chromosomes in the GnomAD database, including 8,710 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 0.32 (8710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48108 AN: 150162 Hom.: 8706 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.320 AC: 48136 AN: 150278 Hom.: 8710 Cov.: 31 AF XY: 0.323 AC XY: 23692 AN XY: 73340

African (AFR) AF: 0.169 AC: 6929 AN: 40904

American (AMR) AF: 0.396 AC: 5993 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 888 AN: 3444

East Asian (EAS) AF: 0.271 AC: 1388 AN: 5130

South Asian (SAS) AF: 0.322 AC: 1511 AN: 4694

European-Finnish (FIN) AF: 0.395 AC: 4075 AN: 10310

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26240 AN: 67386

Other (OTH) AF: 0.318 AC: 664 AN: 2088

Alfa AF: 0.338 Hom.: 1233

Bravo AF: 0.317

Asia WGS AF: 0.326 AC: 1131 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs894363; hg19: chr4-100376846;