rs17773813

Variant names:

• chr4-55142802-G-A
• rs17773813

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 0.252 in 152,040 control chromosomes in the GnomAD database, including 5,259 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 (5259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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: 0.252 AC: 38279 AN: 151922 Hom.: 5261 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.252 AC: 38272 AN: 152040 Hom.: 5259 Cov.: 32 AF XY: 0.250 AC XY: 18562 AN XY: 74318

African (AFR) AF: 0.143 AC: 5936 AN: 41498

American (AMR) AF: 0.229 AC: 3497 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3472

East Asian (EAS) AF: 0.179 AC: 923 AN: 5160

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4812

European-Finnish (FIN) AF: 0.262 AC: 2764 AN: 10538

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21625 AN: 67964

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.280 Hom.: 785

Bravo AF: 0.244

Asia WGS AF: 0.201 AC: 699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.28
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17773813; hg19: chr4-56008969;